Alignments for a candidate for rocA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Shewanella oneidensis MR-1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 202865 SO3774 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file)

Query= reanno::ANA3:7023590
         (1064 letters)



>FitnessBrowser__MR1:202865
          Length = 1059

 Score = 2036 bits (5275), Expect = 0.0
 Identities = 1040/1059 (98%), Positives = 1050/1059 (99%)

Query: 6    MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 65
            MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL
Sbjct: 1    MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 60

Query: 66   VNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 125
            VNKVRQF+KKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA
Sbjct: 61   VNKVRQFEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 120

Query: 126  KWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMA 185
            KWDEHLSKSDSVLVNASTWGLMLTGKIV LDKKIDG+ SNLL RLVNRLGEPVIRQAMMA
Sbjct: 121  KWDEHLSKSDSVLVNASTWGLMLTGKIVSLDKKIDGSSSNLLGRLVNRLGEPVIRQAMMA 180

Query: 186  AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITE 245
            AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYF DYANAITE
Sbjct: 181  AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFTDYANAITE 240

Query: 246  LGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISID 305
            LGAQSYNE+ESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISID
Sbjct: 241  LGAQSYNESESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISID 300

Query: 306  AEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPV 365
            AEEVDRLELSLKLFQKLFN++ATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPV
Sbjct: 301  AEEVDRLELSLKLFQKLFNSEATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPV 360

Query: 366  RLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 425
            RLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN
Sbjct: 361  RLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 420

Query: 426  AQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRR 485
            AQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRR
Sbjct: 421  AQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRR 480

Query: 486  LLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGL 545
            LLENGANTSFVHKLVDPKTPIESLVVHPLKTLT YKTLANNKIVLP DIFGSDRKNSKGL
Sbjct: 481  LLENGANTSFVHKLVDPKTPIESLVVHPLKTLTSYKTLANNKIVLPIDIFGSDRKNSKGL 540

Query: 546  NMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKA 605
            NMNIISEAEPFFAALDKFKSTQWQAGPLVNGQ LTGEHKT+VSPFDTTQTVGQVAFADKA
Sbjct: 541  NMNIISEAEPFFAALDKFKSTQWQAGPLVNGQPLTGEHKTIVSPFDTTQTVGQVAFADKA 600

Query: 606  AIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDE 665
            AIEQAV+SA AAF +WTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDE
Sbjct: 601  AIEQAVSSAHAAFGSWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDE 660

Query: 666  VREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 725
            VREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV
Sbjct: 661  VREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720

Query: 726  SAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIG 785
            SAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIG
Sbjct: 721  SAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIG 780

Query: 786  GVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 845
            GVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS
Sbjct: 781  GVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 840

Query: 846  AGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHI 905
            AGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSS+KTDVGPVIDATAKANLDAHI
Sbjct: 841  AGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSIKTDVGPVIDATAKANLDAHI 900

Query: 906  DHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHV 965
            DHIKQVGKLIKQMSLPAGTENGHFV+PTAVEIDSIKVLEKEHFGPILHVIRYKASELAHV
Sbjct: 901  DHIKQVGKLIKQMSLPAGTENGHFVAPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHV 960

Query: 966  IDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1025
            IDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG
Sbjct: 961  IDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020

Query: 1026 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA 1064
            PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA
Sbjct: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA 1059


Lambda     K      H
   0.317    0.133    0.377 

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: 3144
Number of extensions: 104
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: 1064
Length of database: 1059
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 1014
Effective search space:  1033266
Effective search space used:  1033266
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 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate 202865 SO3774 (proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file))
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.2132.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.9e-222  725.1   1.6   2.5e-222  724.7   1.6    1.1  1  lcl|FitnessBrowser__MR1:202865  SO3774 proline dehydrogenase/del


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202865  SO3774 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.7   1.6  2.5e-222  2.5e-222       1     497 [.     528    1034 ..     528    1037 .. 0.98

  Alignments for each domain:
  == domain 1  score: 724.7 bits;  conditional E-value: 2.5e-222
                       TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaaevq 77  
                                      d++g+ rkns+G+++++ se++++ + l k    ++qa p+v++++   ge + +++p d  + vGqv +ad+a ++
  lcl|FitnessBrowser__MR1:202865  528 DIFGSDRKNSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQPL-TGEHKTIVSPFDTTQTVGQVAFADKAAIE 603 
                                      89****************************************99886.68999************************ PP

                       TIGR01238   78 eavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqvedvld 154 
                                      +av+sa aaf  w+ t+ + ra+ l++ladlle++  el+al+ reaGk++++ i+evreavdf+ryya q+++ ++
  lcl|FitnessBrowser__MR1:202865  604 QAVSSAHAAFGSWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMS 680 
                                      ************************************************************************99998 PP

                       TIGR01238  155 eesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpag 218 
                                      +    +             +G++vcispwnfplaif+Gq++aalaaGntv+akpaeqts+i +rav+l ++aG+p+ 
  lcl|FitnessBrowser__MR1:202865  681 KPELLPgptgelnelflqgRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTD 757 
                                      88777799********************************************************************* PP

                       TIGR01238  219 viqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvl 295 
                                      v+q lpG G++vG alt+deri+Gv ftGst +a+lin++la+re a +pliaetGGqnam+vdst+ +eqvv dv+
  lcl|FitnessBrowser__MR1:202865  758 VLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVV 834 
                                      ***************************************************************************** PP

                       TIGR01238  296 asafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkva 372 
                                      +s+f saGqrcsalrvl++qed+adrv+++++Gamdel++g+p   +tdvGpvida ak nl ahi+++k+++k ++
  lcl|FitnessBrowser__MR1:202865  835 SSSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSIKTDVGPVIDATAKANLDAHIDHIKQVGKLIK 911 
                                      ***************************************************************************** PP

                       TIGR01238  373 qvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqi 449 
                                      q+ l +   +e+g fvapt++e+d+++ l+ke fGp+lhv+ryka+el++v+d+in++G+gltlG+hsr+e+    +
  lcl|FitnessBrowser__MR1:202865  912 QMSLPA--GTENGHFVAPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNEGHALEV 986 
                                      ****99..8999***************************************************************** PP

                       TIGR01238  450 ekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                       ++++vGnvy+nrn++GavvGvqpfGG+GlsGtGpkaGGp+yl r++ 
  lcl|FitnessBrowser__MR1:202865  987 ADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVT 1034
                                      *********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1059 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: 00:00:00.03
# Mc/sec: 13.83
//
[ok]

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

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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