Alignments for a candidate for proC in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for proC in Bradyrhizobium sp. BTAi1

Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_012041982.1 BBTA_RS08100 pyrroline-5-carboxylate reductase

Query= reanno::Caulo:CCNA_00528
         (260 letters)



>NCBI__GCF_000015165.1:WP_012041982.1
          Length = 273

 Score =  190 bits (483), Expect = 2e-53
 Identities = 123/263 (46%), Positives = 157/263 (59%), Gaps = 11/263 (4%)

Query: 3   PILLLGAGRMGGALIQGWQAAGAFDAADLIIRDP----HVDAAAFAGAVVNPPLETLGAA 58
           PI+L GAG+MGGA++ GW  AG  D A +++ +P     + A A  G  +NP   T   A
Sbjct: 13  PIVLAGAGKMGGAMLTGW-LAGGLDPARVVVIEPMPSAEITALAARGIRLNPAAPT--PA 69

Query: 59  KTVLLAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGGRRVARVMPTTAVA 118
           + V++AVKPQ++REA   + P +A   +++SI AG   A +    GG  V R MP T  A
Sbjct: 70  EVVIVAVKPQMFREAGPALKPWVADTTLVLSIMAGTTIASLQNVVGGA-VVRAMPNTPAA 128

Query: 119 IGQG-AASLYADDAEALARAR--ALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFIE 175
           IG+G   ++ A D  A  RA   AL     AV  +  E LM A TAVSGS PAY++   E
Sbjct: 129 IGRGITVAVPASDVSAAQRALTDALLRATGAVEWVDDEALMDAVTAVSGSGPAYVFLLAE 188

Query: 176 ALEAAGAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLM 235
            L  AG A GL  A + RLAR T+ GA  L+ +S    A LR+ VTSPGGTTAAALSVLM
Sbjct: 189 ELARAGIAAGLPEALATRLARDTVSGAGELLHRSELSSATLRQNVTSPGGTTAAALSVLM 248

Query: 236 GAGGFGDLLPKALDAAVARSKEL 258
           G  GF  LL +A+ AA ARSKEL
Sbjct: 249 GPDGFQPLLERAVAAATARSKEL 271


Lambda     K      H
   0.318    0.131    0.366 

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: 182
Number of extensions: 6
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: 260
Length of database: 273
Length adjustment: 25
Effective length of query: 235
Effective length of database: 248
Effective search space:    58280
Effective search space used:    58280
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 WP_012041982.1 BBTA_RS08100 (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.aa/TIGR00112.hmm
# target sequence database:        /tmp/gapView.20980.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.2e-76  242.0   6.1    4.7e-76  241.9   6.1    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012041982.1  BBTA_RS08100 pyrroline-5-carboxy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012041982.1  BBTA_RS08100 pyrroline-5-carboxylate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.9   6.1   4.7e-76   4.7e-76       1     263 []      14     271 ..      14     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 241.9 bits;  conditional E-value: 4.7e-76
                                 TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 
                                               i++ GaG+mg a+l+g+l+ g  ++++++vie+++++    +++ g++ + +   a + a+vv++avKP
  lcl|NCBI__GCF_000015165.1:WP_012041982.1  14 IVLAGAGKMGGAMLTGWLAGG-LDPARVVVIEPMPSAEITALAARGIRLNPA---APTPAEVVIVAVKP 78 
                                               6788***************75.569*********555555555556777766...568899******** PP

                                 TIGR00112  70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138
                                               q+++e+   lk    + ++l++Si+AG+ti+ l++ +++  +vvR+mPNt+a++g+g+t+++  s+vs+
  lcl|NCBI__GCF_000015165.1:WP_012041982.1  79 QMFREAGPALKP-WVADTTLVLSIMAGTTIASLQNVVGG--AVVRAMPNTPAAIGRGITVAVPASDVSA 144
                                               ***********9.666899******************87..8*************************** PP

                                 TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206
                                               +q++l ++ll+a+G v +v+ e+l+davta+sGSgPA+vfll+e la+ag+++GLp+++a++la++t+ 
  lcl|NCBI__GCF_000015165.1:WP_012041982.1 145 AQRALTDALLRATGAVEWVDdEALMDAVTAVSGSGPAYVFLLAEELARAGIAAGLPEALATRLARDTVS 213
                                               ********************************************************************* PP

                                 TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263
                                               Ga++ll++s+ + a+L+++VtsPgGtT+a+l+vL+  + ++  +++av aa++rs+eL
  lcl|NCBI__GCF_000015165.1:WP_012041982.1 214 GAGELLHRSELSSATLRQNVTSPGGTTAAALSVLMGPDgFQPLLERAVAAATARSKEL 271
                                               *********99**********************997544*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (273 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: 8.55
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis