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.21826.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 23.43
//
[ok]

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

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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:

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:

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:

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:

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