Alignments for a candidate for proC in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for proC in Caulobacter crescentus NA1000

Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate CCNA_00528 CCNA_00528 pyrroline-5-carboxylate reductase

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



>FitnessBrowser__Caulo:CCNA_00528
          Length = 260

 Score =  491 bits (1263), Expect = e-144
 Identities = 260/260 (100%), Positives = 260/260 (100%)

Query: 1   MTPILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDAAAFAGAVVNPPLETLGAAKT 60
           MTPILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDAAAFAGAVVNPPLETLGAAKT
Sbjct: 1   MTPILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDAAAFAGAVVNPPLETLGAAKT 60

Query: 61  VLLAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGGRRVARVMPTTAVAIG 120
           VLLAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGGRRVARVMPTTAVAIG
Sbjct: 61  VLLAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGGRRVARVMPTTAVAIG 120

Query: 121 QGAASLYADDAEALARARALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFIEALEAA 180
           QGAASLYADDAEALARARALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFIEALEAA
Sbjct: 121 QGAASLYADDAEALARARALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFIEALEAA 180

Query: 181 GAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLMGAGGF 240
           GAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLMGAGGF
Sbjct: 181 GAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLMGAGGF 240

Query: 241 GDLLPKALDAAVARSKELGG 260
           GDLLPKALDAAVARSKELGG
Sbjct: 241 GDLLPKALDAAVARSKELGG 260


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: 348
Number of extensions: 7
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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 CCNA_00528 CCNA_00528 (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.6806.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-73  232.2   9.0    4.8e-73  232.0   9.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00528  CCNA_00528 pyrroline-5-carboxyla


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00528  CCNA_00528 pyrroline-5-carboxylate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.0   9.0   4.8e-73   4.8e-73       1     263 []       4     258 ..       4     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 232.0 bits;  conditional E-value: 4.8e-73
                             TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdle 73 
                                           i ++GaG+mg al++g++++ga +++++++ +++ ++ aa+   +g+ v+ +  e   +a++vllavKPq ++
  lcl|FitnessBrowser__Caulo:CCNA_00528   4 ILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDA-AAF---AGAVVNPPL-ETLGAAKTVLLAVKPQIWR 71 
                                           679********************88888777644333.222...334445554.5566888************ PP

                             TIGR00112  74 evlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelvee 146
                                           e++a++   + + +++++Si+AGv++++++q++++ +rv+RvmP ta+++g+g+++++a+   ++e  +++++
  lcl|FitnessBrowser__Caulo:CCNA_00528  72 EAIADVVP-HLAPDAVIVSIAAGVRAADISQAFGG-RRVARVMPTTAVAIGQGAASLYAD---DAEALARARA 139
                                           *****999.7779********************86.99*********************9...4567899*** PP

                             TIGR00112 147 llkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgeh 218
                                           l++ ++ v e++ e+l++a+ta+sGS+PA+++ +ieal++ag ++GL+ +++ +la++t++Gaa+l+++sge+
  lcl|FitnessBrowser__Caulo:CCNA_00528 140 LFAPLAAVAELAsEDLMHAATAVSGSAPAYLYAFIEALEAAGAAQGLDPAQSARLARATIIGAAALMAQSGEE 212
                                           ************************************************************************* PP

                             TIGR00112 219 palLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263
                                           pa+L+++VtsPgGtT+a+l+vL+ +g + + + +a++aav+rs+eL
  lcl|FitnessBrowser__Caulo:CCNA_00528 213 PAELRKQVTSPGGTTAAALSVLMGAGgFGDLLPKALDAAVARSKEL 258
                                           **********************98766*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (260 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: 8.95
//
[ok]

This GapMind analysis is from Apr 09 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