Alignments for a candidate for rocA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Acidovorax sp. GW101-3H11

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Ac3H11_2850 Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)

Query= reanno::acidovorax_3H11:Ac3H11_2850
         (1261 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2850
          Length = 1261

 Score = 2471 bits (6405), Expect = 0.0
 Identities = 1261/1261 (100%), Positives = 1261/1261 (100%)

Query: 1    MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60
            MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ
Sbjct: 1    MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60

Query: 61   LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120
            LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR
Sbjct: 61   LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120

Query: 121  DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180
            DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK
Sbjct: 121  DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180

Query: 181  GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240
            GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ
Sbjct: 181  GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240

Query: 241  AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300
            AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG
Sbjct: 241  AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300

Query: 301  LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360
            LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR
Sbjct: 301  LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360

Query: 361  RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420
            RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT
Sbjct: 361  RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420

Query: 421  HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480
            HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC
Sbjct: 421  HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480

Query: 481  RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540
            RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT
Sbjct: 481  RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540

Query: 541  AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600
            AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA
Sbjct: 541  AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600

Query: 601  GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660
            GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL
Sbjct: 601  GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660

Query: 661  EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720
            EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP
Sbjct: 661  EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720

Query: 721  WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780
            WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET
Sbjct: 721  WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780

Query: 781  VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840
            VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL
Sbjct: 781  VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840

Query: 841  VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900
            VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG
Sbjct: 841  VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900

Query: 901  PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960
            PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF
Sbjct: 901  PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960

Query: 961  GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020
            GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG
Sbjct: 961  GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020

Query: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080
            AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL
Sbjct: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080

Query: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140
            APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH
Sbjct: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140

Query: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200
            SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH
Sbjct: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200

Query: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260
            GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI
Sbjct: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260

Query: 1261 G 1261
            G
Sbjct: 1261 G 1261


Lambda     K      H
   0.318    0.133    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 4343
Number of extensions: 160
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1261
Length of database: 1261
Length adjustment: 48
Effective length of query: 1213
Effective length of database: 1213
Effective search space:  1471369
Effective search space used:  1471369
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate Ac3H11_2850 (Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12))
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.5910.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   7.4e-231  752.8   5.5     1e-230  752.4   5.5    1.2  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  Transcriptional repressor of Put


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  Transcriptional repressor of PutA and PutP / Proline dehydrogenase (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  752.4   5.5    1e-230    1e-230       2     499 ..     554    1053 ..     553    1054 .. 0.99

  Alignments for each domain:
  == domain 1  score: 752.4 bits;  conditional E-value: 1e-230
                                        TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadr 61  
                                                       lyg  r+ns G+dl+ne++l +l + l+++a + + aap++    +  g +qpv+npad+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  554 LYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLL-AADVPAGTTQPVRNPADH 612 
                                                       8****************************************.6667889*********** PP

                                        TIGR01238   62 kdivGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallv 121 
                                                       +d+vGqv+ea +a+v++a+  a+aa++ w at+++eraa l r adlle+++  l++ll+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  613 NDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLLEERIQPLMGLLM 672 
                                                       ************************************************************ PP

                                        TIGR01238  122 reaGktlsnaiaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqi 181 
                                                       reaGk+ sna+aevreavdflryya qv+ ++d+ ++ +lG+v cispwnfplaif+Gq+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  673 REAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISPWNFPLAIFMGQV 732 
                                                       ************************************************************ PP

                                        TIGR01238  182 aaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderia 241 
                                                       aaalaaGn v+akpaeqt+liaa+av ll +aGvp +++qllpG+Ge+vGa l  d+r+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  733 AAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGETVGARLIGDARVM 792 
                                                       ************************************************************ PP

                                        TIGR01238  242 GviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeqvvadvlasa 298 
                                                       Gv+ftGstevar +++++a r da    +pliaetGGqnamivds+al eqvv d ++sa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  793 GVMFTGSTEVARILQRTVAGRLDAAgrpIPLIAETGGQNAMIVDSSALVEQVVGDAVSSA 852 
                                                       ***********************97777******************************** PP

                                        TIGR01238  299 fdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnll 358 
                                                       fdsaGqrcsalrvlcvqe+ adrv+++++Gam el+vg+p++l+ dvGpvidaea+  + 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  853 FDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVGPVIDAEAQAGIA 912 
                                                       ************************************************************ PP

                                        TIGR01238  359 ahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykad 418 
                                                       +hiek ka++++v+q   + +  s  gtfv+ptl+el+++ el++evfGpvlh+vry ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  913 QHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVFGPVLHLVRYARS 972 
                                                       ********************99************************************** PP

                                        TIGR01238  419 eldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeG 478 
                                                       +ld+++d+ina+Gyglt Gvh+ri+et++++ +ra++Gnvyvnrn+vGavvGvqpfGGeG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850  973 DLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVGAVVGVQPFGGEG 1032
                                                       ************************************************************ PP

                                        TIGR01238  479 lsGtGpkaGGplylyrltrvr 499 
                                                       lsGtGpkaGGplyl rl++ r
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 1033 LSGTGPKAGGPLYLLRLLSQR 1053
                                                       *****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1261 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 15.10
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources