Alignments for a candidate for xylA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Sinorhizobium meliloti 1021

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate SMc03163 SMc03163 xylose isomerase

Query= reanno::Smeli:SMc03163
         (436 letters)



>FitnessBrowser__Smeli:SMc03163
          Length = 436

 Score =  905 bits (2340), Expect = 0.0
 Identities = 436/436 (100%), Positives = 436/436 (100%)

Query: 1   MSTGFFGDIAKIKYEGPESTNPLAFRHYNPDDVVLGKRMEDHLRFAVAYWHTFVWPGGDP 60
           MSTGFFGDIAKIKYEGPESTNPLAFRHYNPDDVVLGKRMEDHLRFAVAYWHTFVWPGGDP
Sbjct: 1   MSTGFFGDIAKIKYEGPESTNPLAFRHYNPDDVVLGKRMEDHLRFAVAYWHTFVWPGGDP 60

Query: 61  FGGQTFERPWFKDSMEAAKLKADVAFEFFQLLGVPYYCFHDADVRPEGRNFAENTSNLNA 120
           FGGQTFERPWFKDSMEAAKLKADVAFEFFQLLGVPYYCFHDADVRPEGRNFAENTSNLNA
Sbjct: 61  FGGQTFERPWFKDSMEAAKLKADVAFEFFQLLGVPYYCFHDADVRPEGRNFAENTSNLNA 120

Query: 121 IVDYFAGKQGETGVKLLWGTANLFSNRRFMAGAATNPDPDVFAFAAATVKTCIDATQRLD 180
           IVDYFAGKQGETGVKLLWGTANLFSNRRFMAGAATNPDPDVFAFAAATVKTCIDATQRLD
Sbjct: 121 IVDYFAGKQGETGVKLLWGTANLFSNRRFMAGAATNPDPDVFAFAAATVKTCIDATQRLD 180

Query: 181 GENYVLWGGREGYETLLNTDLKRELDQLGRFLNLVVEYKHRIGFKGTILIEPKPQEPTKH 240
           GENYVLWGGREGYETLLNTDLKRELDQLGRFLNLVVEYKHRIGFKGTILIEPKPQEPTKH
Sbjct: 181 GENYVLWGGREGYETLLNTDLKRELDQLGRFLNLVVEYKHRIGFKGTILIEPKPQEPTKH 240

Query: 241 QYDYDVATVYGFLKRYGLENEVKVNIEQGHAILAGHSFEHELALANALGIFGSIDMNRND 300
           QYDYDVATVYGFLKRYGLENEVKVNIEQGHAILAGHSFEHELALANALGIFGSIDMNRND
Sbjct: 241 QYDYDVATVYGFLKRYGLENEVKVNIEQGHAILAGHSFEHELALANALGIFGSIDMNRND 300

Query: 301 YQSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDAKLRRQSIDPEDLLIGHIGGMD 360
           YQSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDAKLRRQSIDPEDLLIGHIGGMD
Sbjct: 301 YQSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDAKLRRQSIDPEDLLIGHIGGMD 360

Query: 361 CCARGLKAAAKMIEDKALSAPLEARYAGWNVPEAKKMLDGGFSLEEIEAWVLKSDVNPQP 420
           CCARGLKAAAKMIEDKALSAPLEARYAGWNVPEAKKMLDGGFSLEEIEAWVLKSDVNPQP
Sbjct: 361 CCARGLKAAAKMIEDKALSAPLEARYAGWNVPEAKKMLDGGFSLEEIEAWVLKSDVNPQP 420

Query: 421 KSGRQELLENVVNRYV 436
           KSGRQELLENVVNRYV
Sbjct: 421 KSGRQELLENVVNRYV 436


Lambda     K      H
   0.320    0.139    0.429 

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: 942
Number of extensions: 25
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
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: 51 (24.3 bits)

Align candidate SMc03163 SMc03163 (xylose isomerase)
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))

# 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/TIGR02630.hmm
# target sequence database:        /tmp/gapView.11525.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02630  [M=435]
Accession:   TIGR02630
Description: xylose_isom_A: xylose isomerase
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-214  697.6   0.0   3.8e-214  697.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc03163  SMc03163 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03163  SMc03163 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  697.4   0.0  3.8e-214  3.8e-214       1     435 []       5     436 .]       5     436 .] 1.00

  Alignments for each domain:
  == domain 1  score: 697.4 bits;  conditional E-value: 3.8e-214
                           TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltdald 75 
                                         ff +i+k+kyeG++s+nplaf++ynp++v+ gk+m+dhlrfavayWht+ + g+DpfG++t+erpw    +d+++
  lcl|FitnessBrowser__Smeli:SMc03163   5 FFGDIAKIKYEGPESTNPLAFRHYNPDDVVLGKRMEDHLRFAVAYWHTFVWPGGDPFGGQTFERPWF---KDSME 76 
                                         799***************************************************************9...58*** PP

                           TIGR02630  76 kakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshpryva 150
                                         +ak k+d+afe+++ lgv+yycfhD+D+ peg++++e+++nl++ivd++  kq etgvklLWgtanlfs++r++a
  lcl|FitnessBrowser__Smeli:SMc03163  77 AAKLKADVAFEFFQLLGVPYYCFHDADVRPEGRNFAENTSNLNAIVDYFAGKQGETGVKLLWGTANLFSNRRFMA 151
                                         *************************************************************************** PP

                           TIGR02630 151 GaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyakkigfkg 225
                                         Gaat+pd+dvfa+aaa+vk+++++t++l genyv+WGGreGyetLlntdlk+eld+l+rfl+l+v+y+++igfkg
  lcl|FitnessBrowser__Smeli:SMc03163 152 GAATNPDPDVFAFAAATVKTCIDATQRLDGENYVLWGGREGYETLLNTDLKRELDQLGRFLNLVVEYKHRIGFKG 226
                                         *************************************************************************** PP

                           TIGR02630 226 qlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGsiDanrgdl 300
                                         ++liePkP+ePtkhqyD+D+atv++flk+y+L++++k+nie+ ha+Lagh+fehel++a++lg++GsiD+nr+d+
  lcl|FitnessBrowser__Smeli:SMc03163 227 TILIEPKPQEPTKHQYDYDVATVYGFLKRYGLENEVKVNIEQGHAILAGHSFEHELALANALGIFGSIDMNRNDY 301
                                         *************************************************************************** PP

                           TIGR02630 301 llGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledg 375
                                         + GWDtD+fp++v e++la+y+vl  gg+++GG+nfdak+rr+s+d+eDll++hi+gmD++arglk+aak++ed+
  lcl|FitnessBrowser__Smeli:SMc03163 302 QSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDAKLRRQSIDPEDLLIGHIGGMDCCARGLKAAAKMIEDK 376
                                         *************************************************************************** PP

                           TIGR02630 376 aleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                         al++ +e ry++++    k++++g  +lee+e+ +l+++ +++ ksgrqelle+++n+y+
  lcl|FitnessBrowser__Smeli:SMc03163 377 ALSAPLEARYAGWNVPEAKKMLDGGFSLEEIEAWVLKSDVNPQPKSGRQELLENVVNRYV 436
                                         **********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (436 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.32
//
[ok]

This GapMind analysis is from Sep 17 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:

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

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 catabolism of small carbon sources