Alignments for a candidate for rocA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Shewanella loihica PV-4

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 5208103 Shew_0615 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)

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



>FitnessBrowser__PV4:5208103
          Length = 1059

 Score = 1848 bits (4786), Expect = 0.0
 Identities = 923/1058 (87%), Positives = 996/1058 (94%)

Query: 6    MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 65
            MFKASEVL GRYDSA LDELF A+T+NYIVDEEQYLSELIKLVPSSD+ I+R+T+RAH+L
Sbjct: 1    MFKASEVLTGRYDSATLDELFTAITNNYIVDEEQYLSELIKLVPSSDDEIQRITKRAHDL 60

Query: 66   VNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 125
            V+KVRQ+DKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALI+DKLSGA
Sbjct: 61   VHKVRQYDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIDDKLSGA 120

Query: 126  KWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMA 185
            KWDEHLSKSDS LVNASTWGLMLTGKI+ LDK IDG PS+LL+RLVNRLGEPVIRQAM+A
Sbjct: 121  KWDEHLSKSDSTLVNASTWGLMLTGKIISLDKSIDGKPSSLLNRLVNRLGEPVIRQAMLA 180

Query: 186  AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITE 245
            AMKIMGKQFVLGRT++EALKNS DKRKLGYTHSYDMLGEAALT KDA+KY+ DY+NAI  
Sbjct: 181  AMKIMGKQFVLGRTVQEALKNSTDKRKLGYTHSYDMLGEAALTMKDAQKYYQDYSNAIAA 240

Query: 246  LGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISID 305
            LGAQ Y+E+E+PRPTISIKLSALHPRYEVANEDR +TELYDT+I+L+  AR LN+G+SID
Sbjct: 241  LGAQQYDESEAPRPTISIKLSALHPRYEVANEDRTMTELYDTLIKLVSQARSLNVGVSID 300

Query: 306  AEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPV 365
            AEEVDRLELSLKLFQKL+N+DA KGWGLLG+VVQAYSKRALPVL W+TRLAK+QGDEIPV
Sbjct: 301  AEEVDRLELSLKLFQKLYNSDAAKGWGLLGLVVQAYSKRALPVLCWITRLAKDQGDEIPV 360

Query: 366  RLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 425
            RLVKGAYWDSELKWAQ AGE  YPL+TRKAGTDVSYLACARYLLSDATRGAIYPQFASHN
Sbjct: 361  RLVKGAYWDSELKWAQVAGEGGYPLFTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 420

Query: 426  AQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRR 485
            AQTVAAI+DMAGDR +EFQRLHGMG+ELYDT+L+E+G   VRIYAP+GAHKDLLPYLVRR
Sbjct: 421  AQTVAAITDMAGDRLYEFQRLHGMGEELYDTLLAESGVSTVRIYAPVGAHKDLLPYLVRR 480

Query: 486  LLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGL 545
            LLENGANTSFVHKLVDPKTPIESLVVHPL TL  YKTLANNKIV P DIFG++RKNSKG+
Sbjct: 481  LLENGANTSFVHKLVDPKTPIESLVVHPLTTLQSYKTLANNKIVQPIDIFGAERKNSKGI 540

Query: 546  NMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKA 605
            NMNIISE+EPFFAALDKFK  QW AGP+VNG+TL+GE   V SP+DTTQ VG+VAFA+  
Sbjct: 541  NMNIISESEPFFAALDKFKDQQWSAGPIVNGETLSGETIEVKSPYDTTQIVGKVAFANNQ 600

Query: 606  AIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDE 665
            AIEQA+ASA  AF +W  TPVEVRA+ALQKLADLLEENREELIALCTREAGKSIQDGIDE
Sbjct: 601  AIEQALASAHNAFGSWCSTPVEVRANALQKLADLLEENREELIALCTREAGKSIQDGIDE 660

Query: 666  VREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 725
            VREAVDFCRYYAVQAKK+M KPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV
Sbjct: 661  VREAVDFCRYYAVQAKKMMGKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720

Query: 726  SAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIG 785
            +AALAAGNTVVAKPAEQTSI+GYRAVQLAH+AGIP + LQ+LPGTGATVG  +TADERIG
Sbjct: 721  TAALAAGNTVVAKPAEQTSIVGYRAVQLAHEAGIPKEALQFLPGTGATVGATITADERIG 780

Query: 786  GVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 845
            GVCFTGST TAK IN TLA R+GAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS
Sbjct: 781  GVCFTGSTVTAKRINLTLAQRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTS 840

Query: 846  AGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHI 905
            AGQRCSALRVL+LQEDIADRVIDV++GAMDEL IGNP SVKTDVGPVIDATAKANL+AHI
Sbjct: 841  AGQRCSALRVLYLQEDIADRVIDVMKGAMDELTIGNPGSVKTDVGPVIDATAKANLNAHI 900

Query: 906  DHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHV 965
            DHIKQVG+LI Q+ LPAGTENGHFV+PTAVEIDSIKVLEKEHFGPILHVIRYKA++L  V
Sbjct: 901  DHIKQVGRLINQLELPAGTENGHFVAPTAVEIDSIKVLEKEHFGPILHVIRYKAADLPKV 960

Query: 966  IDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1025
            ID+INSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG
Sbjct: 961  IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020

Query: 1026 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSD 1063
            PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDS+
Sbjct: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSE 1058


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: 3020
Number of extensions: 101
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 5208103 Shew_0615 (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.9463.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.3e-219  714.9   1.9   3.1e-219  714.5   1.9    1.1  1  lcl|FitnessBrowser__PV4:5208103  Shew_0615 bifunctional proline d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208103  Shew_0615 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.5   1.9  3.1e-219  3.1e-219       1     497 [.     528    1034 ..     528    1037 .. 0.98

  Alignments for each domain:
  == domain 1  score: 714.5 bits;  conditional E-value: 3.1e-219
                        TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaaev 76  
                                       d++g  rkns+G+++++ se +++ + l k  ++++ a piv++++  +ge+  vk+p+d  +ivG+v +a+++ +
  lcl|FitnessBrowser__PV4:5208103  528 DIFGAERKNSKGINMNIISESEPFFAALDKFKDQQWSAGPIVNGET-LSGETIEVKSPYDTTQIVGKVAFANNQAI 602 
                                       89****************************************8765.5688888********************** PP

                        TIGR01238   77 qeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqvedv 152 
                                       ++a+ sa +af  w +t+ + ra  l++ladlle++  el+al+ reaGk++++ i+evreavdf+ryya q+++ 
  lcl|FitnessBrowser__PV4:5208103  603 EQALASAHNAFGSWCSTPVEVRANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKM 678 
                                       **************************************************************************** PP

                        TIGR01238  153 ldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGv 215 
                                       +++    +             +G++vcispwnfplaif+Gq++aalaaGntv+akpaeqts++ +rav+l +eaG+
  lcl|FitnessBrowser__PV4:5208103  679 MGKPELLPgptgelnelflqgRGVFVCISPWNFPLAIFLGQVTAALAAGNTVVAKPAEQTSIVGYRAVQLAHEAGI 754 
                                       *999888899****************************************************************** PP

                        TIGR01238  216 pagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvv 291 
                                       p  ++q+lpG G++vGa++t+deri+Gv ftGst +a++in +la+r+ a +pliaetGGqnam+vdst+ +eqvv
  lcl|FitnessBrowser__PV4:5208103  755 PKEALQFLPGTGATVGATITADERIGGVCFTGSTVTAKRINLTLAQRDGAIIPLIAETGGQNAMVVDSTSQPEQVV 830 
                                       **************************************************************************** PP

                        TIGR01238  292 advlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkak 367 
                                        dv++s+f saGqrcsalrvl++qed+adrv++++kGamdel +g+p+  +tdvGpvida ak nl ahi+++k++
  lcl|FitnessBrowser__PV4:5208103  831 NDVVSSSFTSAGQRCSALRVLYLQEDIADRVIDVMKGAMDELTIGNPGSVKTDVGPVIDATAKANLNAHIDHIKQV 906 
                                       **************************************************************************** PP

                        TIGR01238  368 akkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrie 443 
                                       ++ ++q+ l +   +e+g fvapt++e+d+++ l+ke fGp+lhv+ryka +l kv+d in++G+gltlG+hsr+e
  lcl|FitnessBrowser__PV4:5208103  907 GRLINQLELPA--GTENGHFVAPTAVEIDSIKVLEKEHFGPILHVIRYKAADLPKVIDDINSTGFGLTLGIHSRNE 980 
                                       *********99..8999*********************************************************** PP

                        TIGR01238  444 etvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                       +    + ++++vGnvy+nrn++GavvGvqpfGG+GlsGtGpkaGGp+yl r++ 
  lcl|FitnessBrowser__PV4:5208103  981 GHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVT 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: 00:00:00.04
# Mc/sec: 13.21
//
[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