Alignments for a candidate for PRO3 in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for PRO3 in Shewanella oneidensis MR-1

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate 202462 SO3354 pyrroline-5-carboxylate reductase (NCBI ptt file)

Query= SwissProt::P22008
         (273 letters)



>FitnessBrowser__MR1:202462
          Length = 272

 Score =  214 bits (545), Expect = 2e-60
 Identities = 116/270 (42%), Positives = 170/270 (62%), Gaps = 1/270 (0%)

Query: 1   MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60
           MS  +I FIGAGNM  S+I GL   G PA+Q++A++P   +   +A +F + V + N  A
Sbjct: 1   MSQQKICFIGAGNMTRSIISGLIRSGYPASQVQATNPSQGKLDALATDFGVRVSQDNVSA 60

Query: 61  VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120
             DADV++LSVKPQ M+ VCQAL       +L+++IAAGI  +    +L QP  ++R MP
Sbjct: 61  AQDADVIILSVKPQLMEQVCQALQGIDMSNKLLITIAAGIKASRYSEYLAQPITLIRTMP 120

Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180
           NTP  +  G +GLYA   +S AQ   A +L+S+ G  +W+++E+ I+ V A++GS PAYF
Sbjct: 121 NTPMQIGVGMTGLYAPQSLSDAQKAIAERLMSSGGEIVWVNEESDINQVIALAGSSPAYF 180

Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSS-EVEPAELRRRVTSPNGTTEA 239
           FLLM++M DAG+++G+    A  L  Q ALGAA MA  + E+    LR  VTS  GTT  
Sbjct: 181 FLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPELTLGNLRENVTSKGGTTAQ 240

Query: 240 AIKSFQANGFEALVEQALNAASQRSAELAE 269
           AI +F+A     +V++A+     R+ E+A+
Sbjct: 241 AIATFEAADLRGVVKKAMENCINRAEEMAK 270


Lambda     K      H
   0.315    0.127    0.348 

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: 159
Number of extensions: 7
Number of successful extensions: 2
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: 273
Length of database: 272
Length adjustment: 25
Effective length of query: 248
Effective length of database: 247
Effective search space:    61256
Effective search space used:    61256
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: 47 (22.7 bits)

Align candidate 202462 SO3354 (pyrroline-5-carboxylate reductase (NCBI ptt file))
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.15996.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.9e-78  249.7   6.7    2.2e-78  249.5   6.7    1.0  1  lcl|FitnessBrowser__MR1:202462  SO3354 pyrroline-5-carboxylate r


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202462  SO3354 pyrroline-5-carboxylate reductase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.5   6.7   2.2e-78   2.2e-78       1     263 []       6     268 ..       6     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 249.5 bits;  conditional E-value: 2.2e-78
                       TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlael 79 
                                     i +iGaGnm ++++sgl+++g + ++++  +++s+ kl+ala+++gv+v++d+++a+++adv++l+vKPq +e+v++ l
  lcl|FitnessBrowser__MR1:202462   6 ICFIGAGNMTRSIISGLIRSGYP-ASQVQATNPSQGKLDALATDFGVRVSQDNVSAAQDADVIILSVKPQLMEQVCQAL 83 
                                     68******************888.8****************************************************** PP

                       TIGR00112  80 kseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvveve 158
                                     ++  ++ +klli+i+AG+++++++++l++  +++R mPNt+ ++g g+t+++a +  s++qk+ +e+l+++ G++v+v+
  lcl|FitnessBrowser__MR1:202462  84 QG-IDMSNKLLITIAAGIKASRYSEYLAQPITLIRTMPNTPMQIGVGMTGLYAPQSLSDAQKAIAERLMSSGGEIVWVN 161
                                     **.66699********************99************************************************* PP

                       TIGR00112 159 .eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge.hpalLkdkVtsPgGtTia 235
                                      e+++++v al+GS+PA++fll+e+++dag ++G+++++a++l++q+  Gaa + +++ e +   L+++Vts+gGtT++
  lcl|FitnessBrowser__MR1:202462 162 eESDINQVIALAGSSPAYFFLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPElTLGNLRENVTSKGGTTAQ 240
                                     999******************************************************99999***************** PP

                       TIGR00112 236 glavLeekgvrsavieaveaavkrseeL 263
                                     ++a++e++++r+ v +a+e++++r+ee+
  lcl|FitnessBrowser__MR1:202462 241 AIATFEAADLRGVVKKAMENCINRAEEM 268
                                     *************************986 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.08
//
[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