Alignments for a candidate for PRO3 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for PRO3 in Pseudomonas simiae WCS417

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate GFF5220 PS417_26730 pyrroline-5-carboxylate reductase

Query= SwissProt::P22008
         (273 letters)



>FitnessBrowser__WCS417:GFF5220
          Length = 272

 Score =  373 bits (958), Expect = e-108
 Identities = 193/273 (70%), Positives = 231/273 (84%), Gaps = 1/273 (0%)

Query: 1   MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60
           MS  RIAFIGAGNMAASLIGGLRA+G+ AAQIRASDPGA+ RA++  E  I+    NAEA
Sbjct: 1   MSNTRIAFIGAGNMAASLIGGLRAKGLDAAQIRASDPGADTRARVNTEHGIETFADNAEA 60

Query: 61  VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120
           +   DV+VL+VKPQAMKAVC++L P+L+P QL+VSIAAGI CAS+  WLG  +P+VRCMP
Sbjct: 61  IQGVDVIVLAVKPQAMKAVCESLRPSLQPHQLVVSIAAGITCASMNTWLGA-QPIVRCMP 119

Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180
           NTPAL+ QG SGLYA A+V+A Q +QA +LLSAVGIALWL+ E Q+DAVTAVSGSGPAYF
Sbjct: 120 NTPALVSQGVSGLYATAEVTAEQRDQAHELLSAVGIALWLEQEQQLDAVTAVSGSGPAYF 179

Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240
           FLL++AMT AG KLGLS++ A +L  QTALGAA MA++S+V+ AELRRRVTSP GTT+AA
Sbjct: 180 FLLIEAMTAAGVKLGLSKDVAEQLAEQTALGAAHMAVASDVDAAELRRRVTSPGGTTQAA 239

Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273
           I+SFQA GFEALVE+AL AA+ RSAELAEQLG+
Sbjct: 240 IESFQAGGFEALVEKALGAAAHRSAELAEQLGK 272


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: 256
Number of extensions: 5
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 GFF5220 PS417_26730 (pyrroline-5-carboxylate reductase)
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.617.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    2.3e-83  265.8   8.5    2.6e-83  265.6   8.5    1.0  1  lcl|FitnessBrowser__WCS417:GFF5220  PS417_26730 pyrroline-5-carboxyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5220  PS417_26730 pyrroline-5-carboxylate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.6   8.5   2.6e-83   2.6e-83       1     263 []       6     266 ..       6     266 .. 0.98

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 2.6e-83
                           TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleev 75 
                                         ia+iGaGnm+++l+ gl +kg   +++i   ++ ++ +a+  +e g+e+ +d++ea++  dv++lavKPq +++v
  lcl|FitnessBrowser__WCS417:GFF5220   6 IAFIGAGNMAASLIGGLRAKGLD-AAQIRASDPGADTRARVNTEHGIETFADNAEAIQGVDVIVLAVKPQAMKAV 79 
                                         89**************9999765.8************************************************** PP

                           TIGR00112  76 laelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellka 150
                                         +++l+  + + ++l++Si+AG+t++ ++++l+a +++vR+mPNt+a v +gv++++a++ev++eq+++++ell+a
  lcl|FitnessBrowser__WCS417:GFF5220  80 CESLRP-SLQPHQLVVSIAAGITCASMNTWLGA-QPIVRCMPNTPALVSQGVSGLYATAEVTAEQRDQAHELLSA 152
                                         *****9.7779********************86.99*************************************** PP

                           TIGR00112 151 vGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkd 224
                                         vG ++++e e++ldavta+sGSgPA++flliea+ +agvklGL+++ a++la qt  Gaa++   s+ ++a+L+ 
  lcl|FitnessBrowser__WCS417:GFF5220 153 VGIALWLEqEQQLDAVTAVSGSGPAYFFLLIEAMTAAGVKLGLSKDVAEQLAEQTALGAAHMAVASDVDAAELRR 227
                                         *************************************************************************** PP

                           TIGR00112 225 kVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263
                                         +VtsPgGtT+a++++++++g+++ v++a+ aa++rs eL
  lcl|FitnessBrowser__WCS417:GFF5220 228 RVTSPGGTTQAAIESFQAGGFEALVEKALGAAAHRSAEL 266
                                         ************************************997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.15
//
[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