GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proC in Sphingomonas indica Dd16

Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_085219465.1 B9N75_RS07535 pyrroline-5-carboxylate reductase

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



>NCBI__GCF_900177405.1:WP_085219465.1
          Length = 269

 Score =  177 bits (449), Expect = 2e-49
 Identities = 105/260 (40%), Positives = 143/260 (55%), Gaps = 5/260 (1%)

Query: 3   PILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDAAAFAGAVVNPPLETLGAAKTVL 62
           P  ++G G M GA+++GW AAG       +IR     A      +   P +   A    +
Sbjct: 7   PFWMIGCGNMAGAMLEGWLAAGLDPDRVTVIRPSGTPAPGGVRTLTALPADETPAI--AM 64

Query: 63  LAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGG-RRVARVMPTTAVAIGQ 121
           L VKPQ   +    + P LAP+ ++VSI AGV  A +   F   R + R MP T VA+ +
Sbjct: 65  LGVKPQKLDDVAPSLAPALAPETILVSILAGVETASLRARFAAPRTIVRAMPNTPVALRK 124

Query: 122 GAASLYADDAEALARAR--ALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFIEALEA 179
           GA  L++D A   AR    AL   L     +  EDL+H   A+ GS PA+++ FI+A+ A
Sbjct: 125 GATGLFSDSAHPAAREAVGALMTALGHAEWVEDEDLLHVVGALCGSGPAFVFRFIDAIAA 184

Query: 180 AGAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLMGAGG 239
           AGAA GL P Q+ARLA AT+ GA +L   S E P EL  +VTSPGG TA  L +L     
Sbjct: 185 AGAALGLPPEQAARLALATVDGAGSLAGSSPETPHELAVRVTSPGGMTAKGLDILDDDAA 244

Query: 240 FGDLLPKALDAAVARSKELG 259
             DL+ + L+AAV RS+E+G
Sbjct: 245 LADLVRRTLEAAVDRSREMG 264


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: 198
Number of extensions: 7
Number of successful extensions: 4
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: 269
Length adjustment: 25
Effective length of query: 235
Effective length of database: 244
Effective search space:    57340
Effective search space used:    57340
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_085219465.1 B9N75_RS07535 (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.1964618.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-65  206.6   0.0    3.2e-65  206.4   0.0    1.1  1  NCBI__GCF_900177405.1:WP_085219465.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085219465.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   0.0   3.2e-65   3.2e-65       3     263 .]      10     263 ..       8     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 3.2e-65
                             TIGR00112   3 iiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleev 75 
                                           +iG+Gnm+ a+l+g+l++g   ++++ vi++s + +   + +l +  + +         + +l+vKPq+l++v
  NCBI__GCF_900177405.1:WP_085219465.1  10 MIGCGNMAGAMLEGWLAAGLD-PDRVTVIRPSGTPAPGGVRTLTALPADE------TPAIAMLGVKPQKLDDV 75 
                                           79***************9775.9********9999888888875444443......445779*********** PP

                             TIGR00112  76 laelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveell 148
                                           + +l+    + e++l+SilAGv+++ l+  ++a +++vR+mPNt++++++g+t+++ +  ++++ +e v +l+
  NCBI__GCF_900177405.1:WP_085219465.1  76 APSLAP-ALAPETILVSILAGVETASLRARFAAPRTIVRAMPNTPVALRKGATGLFSD-SAHPAAREAVGALM 146
                                           *****9.6669*********************************************99.588999******** PP

                             TIGR00112 149 kavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpa 220
                                           +a+G++ +ve e+ll+ v al+GSgPAfvf +i+a+a+ag +lGLp e+a +la +t+ Ga+ l   s e+p 
  NCBI__GCF_900177405.1:WP_085219465.1 147 TALGHAEWVEdEDLLHVVGALCGSGPAFVFRFIDAIAAAGAALGLPPEQAARLALATVDGAGSLAGSSPETPH 219
                                           ************************************************************************* PP

                             TIGR00112 221 lLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263
                                           +L  +VtsPgG T++gl +L +++ + + v +++eaav+rs+e+
  NCBI__GCF_900177405.1:WP_085219465.1 220 ELAVRVTSPGGMTAKGLDILDDDAaLADLVRRTLEAAVDRSREM 263
                                           ********************988769***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (269 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: 17.13
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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