GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Oceanisphaera arctica V1-41

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_104486877.1 UN63_RS11415 branched-chain amino acid transaminase

Query= BRENDA::P0AB80
         (309 letters)



>NCBI__GCF_002936955.1:WP_104486877.1
          Length = 307

 Score =  431 bits (1108), Expect = e-125
 Identities = 197/302 (65%), Positives = 248/302 (82%)

Query: 6   ADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSA 65
           A YIWFNG+MV WE A+VHVMSHALHYG+SVFEGIR Y++ +GP++FR  EH+QRL DSA
Sbjct: 4   AKYIWFNGDMVPWEKAQVHVMSHALHYGSSVFEGIRAYETPRGPMIFRLEEHVQRLFDSA 63

Query: 66  KIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAF 125
           KIYR  +  + +ELM+ACR  + +N L SAY+RPL+F+G+VGMG+N P     DVI+AA 
Sbjct: 64  KIYRMKIPYTHEELMDACRKAVSENELNSAYLRPLVFIGNVGMGLNAPKDVPCDVIVAAI 123

Query: 126 PWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIA 185
           PWGAYLG E LE+G+D  V+SWNR APNT+PT AKAGGNYLSS L+  EA+RHGY EGI+
Sbjct: 124 PWGAYLGEEGLERGVDVCVTSWNRLAPNTMPTGAKAGGNYLSSQLISGEAKRHGYDEGIS 183

Query: 186 LDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRE 245
           LDV+G++SEGAGENLF +K+ VL+TPP T+  LPGITRD ++ LA+E G +VRE+ +SRE
Sbjct: 184 LDVHGHLSEGAGENLFLIKNKVLYTPPVTACILPGITRDTLMTLAREAGYQVREEAISRE 243

Query: 246 SLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLD 305
           +LYLADE+FM+GTAAE+TPVRSVDGI++G G+ GP+T  +Q+AFFGLF G T DKWGWL 
Sbjct: 244 ALYLADEMFMTGTAAEVTPVRSVDGIELGAGKRGPITTELQKAFFGLFDGSTRDKWGWLT 303

Query: 306 QV 307
            V
Sbjct: 304 PV 305


Lambda     K      H
   0.319    0.136    0.413 

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: 365
Number of extensions: 9
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: 309
Length of database: 307
Length adjustment: 27
Effective length of query: 282
Effective length of database: 280
Effective search space:    78960
Effective search space used:    78960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_104486877.1 UN63_RS11415 (branched-chain amino acid transaminase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.3170514.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-139  449.1   0.0   3.8e-139  448.9   0.0    1.0  1  NCBI__GCF_002936955.1:WP_104486877.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002936955.1:WP_104486877.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.9   0.0  3.8e-139  3.8e-139       1     298 []       8     305 ..       8     305 .. 1.00

  Alignments for each domain:
  == domain 1  score: 448.9 bits;  conditional E-value: 3.8e-139
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           w++G++v++e a+vhv++halhYG++vfeGiRaYet++g++ifrl+ehv+Rl+dsaki+r++ipy++eel+++
  NCBI__GCF_002936955.1:WP_104486877.1   8 WFNGDMVPWEKAQVHVMSHALHYGSSVFEGIRAYETPRGPMIFRLEEHVQRLFDSAKIYRMKIPYTHEELMDA 80 
                                           9************************************************************************ PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           +++++ +n+l+saY+Rplv++G+ ++gl+++ d++ +vi+aa++wgaylgee+le+G++v v+s++r a+n++
  NCBI__GCF_002936955.1:WP_104486877.1  81 CRKAVSENELNSAYLRPLVFIGNVGMGLNAPKDVPCDVIVAAIPWGAYLGEEGLERGVDVCVTSWNRLAPNTM 153
                                           ************************************************************************* PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           pt aka+gnYl+s+l+  ea+r+Gyde+i Ld +G+++eG+Gen+f++k+ vl+tPpv+  iL gitrd++++
  NCBI__GCF_002936955.1:WP_104486877.1 154 PTGAKAGGNYLSSQLISGEAKRHGYDEGISLDVHGHLSEGAGENLFLIKNKVLYTPPVTACILPGITRDTLMT 226
                                           ************************************************************************* PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292
                                           la+e g++v+ee isre+ly+aDe+f+tGtaaevtP+r+vDg+++g+gkrGp+t +lq+aff l+ g t++k+
  NCBI__GCF_002936955.1:WP_104486877.1 227 LAREAGYQVREEAISREALYLADEMFMTGTAAEVTPVRSVDGIELGAGKRGPITTELQKAFFGLFDGSTRDKW 299
                                           ************************************************************************* PP

                             TIGR01122 293 ewltyv 298
                                           +wlt+v
  NCBI__GCF_002936955.1:WP_104486877.1 300 GWLTPV 305
                                           ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (307 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: 24.94
//
[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