GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Amantichitinum ursilacus IGB-41

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_053938794.1 WG78_RS15740 pyrroline-5-carboxylate reductase

Query= SwissProt::P22008
         (273 letters)



>NCBI__GCF_001294205.1:WP_053938794.1
          Length = 272

 Score =  212 bits (539), Expect = 8e-60
 Identities = 117/269 (43%), Positives = 169/269 (62%), Gaps = 2/269 (0%)

Query: 5   RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64
           +I FIG GNMA +LIGG+  QG  A Q+   +P A +R ++  EF + V   +A   A +
Sbjct: 2   KITFIGGGNMAGALIGGMTQQGFSADQLHVVEPDAARRDQLVEEFGVSVSAPDAPRPA-S 60

Query: 65  DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124
           DVV+ +VKPQ ++ V QA A     + L++SIAAG+   ++  WL   R +VR MPNTPA
Sbjct: 61  DVVIFAVKPQQLRPVVQA-ALQNGDQPLLISIAAGVRAETISRWLDGYRRIVRVMPNTPA 119

Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184
           L+R G SGLYA  +V+A     + ++ +++G  +WLD+E+QID +TA+SGSGPAY F  M
Sbjct: 120 LVRAGMSGLYAAPEVNAEDRALSERIFTSIGKTVWLDEESQIDGLTAISGSGPAYVFYFM 179

Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244
           +A+  A    G S + A  L  QT  G+ ++AL S+ + A LR +VTS  GTTE AI +F
Sbjct: 180 EALQAAARAQGFSPDVAHLLAYQTVAGSVKLALESDDDAATLRVKVTSKGGTTERAINAF 239

Query: 245 QANGFEALVEQALNAASQRSAELAEQLGQ 273
           + +   A +  A  AA+ RS EL E+LG+
Sbjct: 240 ENSQMRATIIAAAAAAAARSRELGEELGR 268


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: 177
Number of extensions: 9
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 WP_053938794.1 WG78_RS15740 (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.3247705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.6e-82  261.1   0.7    7.4e-82  260.9   0.7    1.0  1  NCBI__GCF_001294205.1:WP_053938794.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053938794.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.9   0.7   7.4e-82   7.4e-82       1     263 []       3     262 ..       3     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 260.9 bits;  conditional E-value: 7.4e-82
                             TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdle 73 
                                           i++iG+Gnm+ al+ g+ ++g + +++++v+e+ ++++++l++e+gv+v++++ +   ++dvv++avKPq+l+
  NCBI__GCF_001294205.1:WP_053938794.1   3 ITFIGGGNMAGALIGGMTQQGFS-ADQLHVVEPDAARRDQLVEEFGVSVSAPD-APRPASDVVIFAVKPQQLR 73 
                                           79*****************9887.8*************************995.6777999************ PP

                             TIGR00112  74 evlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelvee 146
                                           +v++   +  +  + lliSi+AGv++e+++++l++ +r+vRvmPNt+a v+ag+++++a  ev++e+++l e+
  NCBI__GCF_001294205.1:WP_053938794.1  74 PVVQAALQ--NGDQPLLISIAAGVRAETISRWLDGYRRIVRVMPNTPALVRAGMSGLYAAPEVNAEDRALSER 144
                                           ***96555..5579*********************************************************** PP

                             TIGR00112 147 llkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgeh 218
                                           +++++Gk+v+++ e+++d +ta+sGSgPA+vf+++eal++a+ ++G++ + a  la+qt++G++kl  es+++
  NCBI__GCF_001294205.1:WP_053938794.1 145 IFTSIGKTVWLDeESQIDGLTAISGSGPAYVFYFMEALQAAARAQGFSPDVAHLLAYQTVAGSVKLALESDDD 217
                                           ************99*********************************************************** PP

                             TIGR00112 219 palLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263
                                           +a+L+ kVts+gGtT ++++++e++++r+++i+a  aa++rs+eL
  NCBI__GCF_001294205.1:WP_053938794.1 218 AATLRVKVTSKGGTTERAINAFENSQMRATIIAAAAAAAARSREL 262
                                           ******************************************998 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: 24.41
//
[ok]

This GapMind analysis is from Sep 24 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:

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:

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:

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:

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