Alignments for a candidate for rocA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Shewanella amazonensis SB2B

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 6938573 Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= reanno::SB2B:6938573
         (1058 letters)



>FitnessBrowser__SB2B:6938573
          Length = 1058

 Score = 2068 bits (5357), Expect = 0.0
 Identities = 1058/1058 (100%), Positives = 1058/1058 (100%)

Query: 1    MFKASEVLAGRYDNANLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDL 60
            MFKASEVLAGRYDNANLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDL
Sbjct: 1    MFKASEVLAGRYDNANLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDL 60

Query: 61   VAKVRQYEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGA 120
            VAKVRQYEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGA
Sbjct: 61   VAKVRQYEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGA 120

Query: 121  KWDEHMSKSDSVLVNASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYA 180
            KWDEHMSKSDSVLVNASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYA
Sbjct: 121  KWDEHMSKSDSVLVNASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYA 180

Query: 181  AMKIMGKQFVLGRTIEEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQA 240
            AMKIMGKQFVLGRTIEEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQA
Sbjct: 181  AMKIMGKQFVLGRTIEEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQA 240

Query: 241  LGTAKFDESEAPRPTISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQID 300
            LGTAKFDESEAPRPTISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQID
Sbjct: 241  LGTAKFDESEAPRPTISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQID 300

Query: 301  AEEVDRLELSLKLFKKLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPL 360
            AEEVDRLELSLKLFKKLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPL
Sbjct: 301  AEEVDRLELSLKLFKKLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPL 360

Query: 361  RLVKGAYWDSELKWAQQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHN 420
            RLVKGAYWDSELKWAQQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHN
Sbjct: 361  RLVKGAYWDSELKWAQQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHN 420

Query: 421  AQTVAAITAMVGDRKFEFQRLHGMGQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRR 480
            AQTVAAITAMVGDRKFEFQRLHGMGQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRR
Sbjct: 421  AQTVAAITAMVGDRKFEFQRLHGMGQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRR 480

Query: 481  LLENGANTSFVHKLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGL 540
            LLENGANTSFVHKLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGL
Sbjct: 481  LLENGANTSFVHKLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGL 540

Query: 541  NMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEA 600
            NMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEA
Sbjct: 541  NMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEA 600

Query: 601  TIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDE 660
            TIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDE
Sbjct: 601  TIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDE 660

Query: 661  VREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720
            VREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV
Sbjct: 661  VREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720

Query: 721  AAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIG 780
            AAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIG
Sbjct: 721  AAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIG 780

Query: 781  GVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTS 840
            GVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTS
Sbjct: 781  GVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTS 840

Query: 841  AGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHI 900
            AGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHI
Sbjct: 841  AGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHI 900

Query: 901  DHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKV 960
            DHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKV
Sbjct: 901  DHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKV 960

Query: 961  IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020
            IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG
Sbjct: 961  IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020

Query: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDAD 1058
            PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDAD
Sbjct: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDAD 1058


Lambda     K      H
   0.317    0.134    0.380 

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: 3068
Number of extensions: 91
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: 1058
Length of database: 1058
Length adjustment: 45
Effective length of query: 1013
Effective length of database: 1013
Effective search space:  1026169
Effective search space used:  1026169
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: 58 (26.9 bits)

Align candidate 6938573 Sama_2676 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq))
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.7169.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.4e-218  711.1   1.2   4.6e-218  710.6   1.2    1.2  1  lcl|FitnessBrowser__SB2B:6938573  Sama_2676 bifunctional proline d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938573  Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  710.6   1.2  4.6e-218  4.6e-218       1     497 [.     528    1034 ..     528    1037 .. 0.98

  Alignments for each domain:
  == domain 1  score: 710.6 bits;  conditional E-value: 4.6e-218
                         TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaae 75  
                                        d++g  rkns+G+++++ se +++ + l+k  + ++ a p+v+++   +ge++ v++p++   +vGqv +a++a+
  lcl|FitnessBrowser__SB2B:6938573  528 DIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSAGPLVNGE-TLSGEVRDVVSPYNTTLKVGQVAFANEAT 601 
                                        89****************************************766.5689************************* PP

                         TIGR01238   76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqve 150 
                                        +++a+  a +afa w  t+ + ra  l++ladlle++  el+al+ reaGk++++ i+evreavdf+ryya q++
  lcl|FitnessBrowser__SB2B:6938573  602 IEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAK 676 
                                        **************************************************************************9 PP

                         TIGR01238  151 dvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqe 212 
                                        + +++    +             +G++vcispwnfplaif+Gq+aaala+Gntviakpaeqt li  rav+l +e
  lcl|FitnessBrowser__SB2B:6938573  677 KMMSKPELLPgptgelnelflqgRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQLAHE 751 
                                        999998777799*************************************************************** PP

                         TIGR01238  213 aGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstala 287 
                                        aG+p  v+q+lpG G+ vGa ltsderi+Gv ftGst +a+ in+ala r+ a +pliaetGGqnam+vdst+ +
  lcl|FitnessBrowser__SB2B:6938573  752 AGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQP 826 
                                        *************************************************************************** PP

                         TIGR01238  288 eqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahie 362 
                                        eqvv dv++saf saGqrcsalrvl++qed+a+rvl+++kGamdel +g+p+  +tdvGpvida ak nl ahi+
  lcl|FitnessBrowser__SB2B:6938573  827 EQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHID 901 
                                        *************************************************************************** PP

                         TIGR01238  363 kmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlG 437 
                                        ++k++++ ++q+ l +   +e+g fvapt++e+d+++ l ke fGp+lhvvryka  l+kv+d in++G+gltlG
  lcl|FitnessBrowser__SB2B:6938573  902 HIKQVGRLIHQLSLPE--GTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLG 974 
                                        **************99..8999***************************************************** PP

                         TIGR01238  438 vhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                        +hsr+e+    + ++++vGnvy+nrn++GavvGvqpfGG+GlsGtGpkaGGp+yl r++ 
  lcl|FitnessBrowser__SB2B:6938573  975 IHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVT 1034
                                        *********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1058 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: 20.26
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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