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 5208627 Shew_1136 pyrroline-5-carboxylate reductase (RefSeq)

Query= curated2:P52053
         (272 letters)



>FitnessBrowser__PV4:5208627
          Length = 272

 Score =  276 bits (707), Expect = 3e-79
 Identities = 142/272 (52%), Positives = 186/272 (68%)

Query: 1   MEHKKIAFIGAGNMVRAIVSGLVANGYPAQNITATAPSEARRLPLEQDFGIRTTSDNIQA 60
           M  KKI FIGAGNM R+I SGLV  GY  + I AT PSE + + L+QD GIR + DN+QA
Sbjct: 1   MTQKKICFIGAGNMTRSITSGLVKGGYAPELIHATNPSEGKLIALKQDLGIRVSHDNLQA 60

Query: 61  ATEADVVVLSVKPQMMADVCKPLQAIDFTNKLVISIAAGINCSRLDDMLATKLNLVRVMP 120
           A EADV+VL+VKPQ+M  VC+ +  ++  +KL+++IAAG+   R        + L+R MP
Sbjct: 61  ADEADVIVLAVKPQLMQQVCEAMSGLNLKDKLIVTIAAGVTAERYHAFFKQPIQLIRTMP 120

Query: 121 NTPSQLGLGMSGLFAPIHVTEHDKAFAAELMEAVGKVCWVEQESGINNVIAAAGSAPAYF 180
           NTP+Q+GLGM+GL+A   V+  D+    +LM+  G+  WVE+E  +N VIA AGS+PAYF
Sbjct: 121 NTPTQIGLGMTGLYAEQGVSAQDRELCEQLMQTGGETVWVEKEEDLNQVIALAGSSPAYF 180

Query: 181 FLFMEAMQAEAIAQGFDKESARLLVQQAALGAASMVVSNPETELSTLRENVTSKGGTTAE 240
           FL MEAM   A   G D+++AR +VQQAALGAA+MV  NP+   + LRENVTSKGGTTA+
Sbjct: 181 FLMMEAMIDSAKQDGVDEQTAREMVQQAALGAAAMVKQNPQLSPAQLRENVTSKGGTTAQ 240

Query: 241 ALRTFNEHQLSDIVAKAMQAAVARAEEMEKLF 272
           AL  F    L +IV  AM   + RA+EM K F
Sbjct: 241 ALAAFERAGLREIVRTAMHDCMDRAQEMAKQF 272


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: 212
Number of extensions: 8
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: 272
Length of database: 272
Length adjustment: 25
Effective length of query: 247
Effective length of database: 247
Effective search space:    61009
Effective search space used:    61009
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 5208627 Shew_1136 (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.23518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    8.3e-78  247.6   4.5    9.3e-78  247.5   4.5    1.0  1  lcl|FitnessBrowser__PV4:5208627  Shew_1136 pyrroline-5-carboxylat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208627  Shew_1136 pyrroline-5-carboxylate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.5   4.5   9.3e-78   9.3e-78       1     263 []       6     268 ..       6     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 247.5 bits;  conditional E-value: 9.3e-78
                        TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlae 78 
                                      i +iGaGnm +++ sgl+k g  a++ i+ +++se kl al ++lg++v++d+ +a++eadv++lavKPq +++v++ 
  lcl|FitnessBrowser__PV4:5208627   6 ICFIGAGNMTRSITSGLVKGGY-APELIHATNPSEGKLIALKQDLGIRVSHDNLQAADEADVIVLAVKPQLMQQVCEA 82 
                                      68****************9755.59****************************************************9 PP

                        TIGR00112  79 lkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvve 156
                                      + +  + k+kl+++i+AGvt+e+++  +++  +++R mPNt+ ++g g+t+++a++ vs++++el e+l+++ G++v+
  lcl|FitnessBrowser__PV4:5208627  83 MSG-LNLKDKLIVTIAAGVTAERYHAFFKQPIQLIRTMPNTPTQIGLGMTGLYAEQGVSAQDRELCEQLMQTGGETVW 159
                                      999.7779*********************99*********************************************** PP

                        TIGR00112 157 ve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge.hpalLkdkVtsPgGt 232
                                      ve e++l++v al+GS+PA++fl++ea++d++ + G ++++a+e+++q+  Gaa++++++ + +pa+L+++Vts+gGt
  lcl|FitnessBrowser__PV4:5208627 160 VEkEEDLNQVIALAGSSPAYFFLMMEAMIDSAKQDGVDEQTAREMVQQAALGAAAMVKQNPQlSPAQLRENVTSKGGT 237
                                      ***********************************************************9889*************** PP

                        TIGR00112 233 TiaglavLeekgvrsavieaveaavkrseeL 263
                                      T+++la++e++g+r+ v  a++ +++r++e+
  lcl|FitnessBrowser__PV4:5208627 238 TAQALAAFERAGLREIVRTAMHDCMDRAQEM 268
                                      ****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (272 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 7.36
//
[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