Alignments for a candidate for PRO3 in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for PRO3 in Shewanella loihica PV-4

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate 5210588 Shew_3016 pyrroline-5-carboxylate reductase (RefSeq)

Query= curated2:P52053
         (272 letters)



>FitnessBrowser__PV4:5210588
          Length = 264

 Score =  194 bits (494), Expect = 1e-54
 Identities = 109/262 (41%), Positives = 159/262 (60%), Gaps = 8/262 (3%)

Query: 14  MVRAIVSGLVANGYPAQNITATAPSEARRLPLEQDFGIRTTSDNIQAATEADVVVLSVKP 73
           M  AI+ GL+ +G+ + +I   APS+  R  L QDF +R  SDN  A   AD+++L+VKP
Sbjct: 1   MASAIIRGLIKHGHRSAHILVCAPSQRTRSRLVQDFNVRVHSDNSAAVAFADIIILAVKP 60

Query: 74  QMMADVCKPLQAI-------DFTNKLVISIAAGINCSRLDDMLATKLNLVRVMPNTPSQL 126
            ++  VC  L+ +           KL+ISIAAG+  + + D L   + LV  MPN P+ +
Sbjct: 61  FIVPLVCDELRPLLGQVNNGRSEQKLLISIAAGLTHASISDKLPQNVQLVCAMPNLPTAI 120

Query: 127 GLGMSGLFAPIHVTEHDKAFAAELMEAVGKVCWVEQESGINNVIAAAGSAPAYFFLFMEA 186
           G G++GLF P H+       A +LM AVG   W+E E  + +++A AGS+PAYFFLF+EA
Sbjct: 121 GKGLTGLFVPGHLDRQAVDDAEQLMRAVGDTVWLEDEQQMASIVATAGSSPAYFFLFLEA 180

Query: 187 MQAEAIAQGFDKESARLLVQQAALGAASMVVSNPETELSTLRENVTSKGGTTAEALRTFN 246
           M+  AIAQG   ++A   V Q+A+GA SM +++ E  L+ LR  VTS  GTT +A+  F 
Sbjct: 181 MEKAAIAQGLPAKTASKAVLQSAMGAVSMAMASKE-GLANLRHQVTSPKGTTEQAVLAFQ 239

Query: 247 EHQLSDIVAKAMQAAVARAEEM 268
              L  +VA+AM +A  RA+E+
Sbjct: 240 HGDLDALVARAMDSAARRAKEL 261


Lambda     K      H
   0.317    0.129    0.353 

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: 128
Number of extensions: 4
Number of successful extensions: 3
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: 272
Length of database: 264
Length adjustment: 25
Effective length of query: 247
Effective length of database: 239
Effective search space:    59033
Effective search space used:    59033
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: 47 (22.7 bits)

Align candidate 5210588 Shew_3016 (pyrroline-5-carboxylate reductase (RefSeq))
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))

# 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/TIGR00112.hmm
# target sequence database:        /tmp/gapView.5068.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00112  [M=263]
Accession:   TIGR00112
Description: proC: pyrroline-5-carboxylate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    3.8e-71  225.8   2.3    4.2e-71  225.6   2.3    1.0  1  lcl|FitnessBrowser__PV4:5210588  Shew_3016 pyrroline-5-carboxylat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210588  Shew_3016 pyrroline-5-carboxylate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.6   2.3   4.2e-71   4.2e-71       9     263 .]       1     261 [.       1     261 [. 0.98

  Alignments for each domain:
  == domain 1  score: 225.6 bits;  conditional E-value: 4.2e-71
                        TIGR00112   9 mgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlaelks..... 81 
                                      m++a+++gl+k+g + +++ilv+++s+  + +l+++++v+v+sd+ +av+ ad+++lavKP  ++ v+ el+      
  lcl|FitnessBrowser__PV4:5210588   1 MASAIIRGLIKHGHR-SAHILVCAPSQRTRSRLVQDFNVRVHSDNSAAVAFADIIILAVKPFIVPLVCDELRPllgqv 77 
                                      9***********988.89****************************************************99888887 PP

                        TIGR00112  82 .eektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvveve 158
                                       + ++++klliSi+AG+t + ++++l+++ ++v +mPN++ ++g+g t+++   + + +  + +e+l++avG++v++e
  lcl|FitnessBrowser__PV4:5210588  78 nNGRSEQKLLISIAAGLTHASISDKLPQNVQLVCAMPNLPTAIGKGLTGLFVPGHLDRQAVDDAEQLMRAVGDTVWLE 155
                                      777899************************************************************************ PP

                        TIGR00112 159 .eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVtsPgGtTia 235
                                       e+++  ++a +GS+PA++fl++ea+++a++++GLp+++a +++ q  +Ga+ + + s+e  a L+++VtsP+GtT +
  lcl|FitnessBrowser__PV4:5210588 156 dEQQMASIVATAGSSPAYFFLFLEAMEKAAIAQGLPAKTASKAVLQSAMGAVSMAMASKEGLANLRHQVTSPKGTTEQ 233
                                      ****************************************************************************** PP

                        TIGR00112 236 glavLeekgvrsavieaveaavkrseeL 263
                                      ++ +++++++ + v++a+++a++r++eL
  lcl|FitnessBrowser__PV4:5210588 234 AVLAFQHGDLDALVARAMDSAARRAKEL 261
                                      **************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (264 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 7.83
//
[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:

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