Alignments for a candidate for xylA in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Rhizobium leguminosarum 3841

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate WP_003552938.1 RL_RS21535 xylose isomerase

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



>NCBI__GCF_000009265.1:WP_003552938.1
          Length = 436

 Score =  801 bits (2070), Expect = 0.0
 Identities = 378/436 (86%), Positives = 406/436 (93%)

Query: 1   MSTGFFGDIAKIKYEGPESTNPLAFRHYNPDDVVLGKRMEDHLRFAVAYWHTFVWPGGDP 60
           MSTGFFGDI K+KYEGP+STNPLAFRHY PD++V+GKRMEDHLRFAVAYWHTF WPGGDP
Sbjct: 1   MSTGFFGDIQKVKYEGPDSTNPLAFRHYQPDEIVMGKRMEDHLRFAVAYWHTFTWPGGDP 60

Query: 61  FGGQTFERPWFKDSMEAAKLKADVAFEFFQLLGVPYYCFHDADVRPEGRNFAENTSNLNA 120
           FGGQTF RPWF+D+M+AAKLKADVAFEFF LLG PYYCFHDADVRPEG+ FAENT NLN 
Sbjct: 61  FGGQTFLRPWFEDTMKAAKLKADVAFEFFSLLGSPYYCFHDADVRPEGKTFAENTKNLNE 120

Query: 121 IVDYFAGKQGETGVKLLWGTANLFSNRRFMAGAATNPDPDVFAFAAATVKTCIDATQRLD 180
           IVDYFA KQ  TG KLLWGTANLFS+RR+M+GAATNPDPDVFAFAAATVKTCIDATQ+L 
Sbjct: 121 IVDYFAEKQAATGTKLLWGTANLFSHRRYMSGAATNPDPDVFAFAAATVKTCIDATQKLG 180

Query: 181 GENYVLWGGREGYETLLNTDLKRELDQLGRFLNLVVEYKHRIGFKGTILIEPKPQEPTKH 240
           GENYVLWGGREGYETLLNTD+ RELDQLGRFLNLVVEYKH+IG+KGTILIEPKPQEPTKH
Sbjct: 181 GENYVLWGGREGYETLLNTDIGRELDQLGRFLNLVVEYKHKIGYKGTILIEPKPQEPTKH 240

Query: 241 QYDYDVATVYGFLKRYGLENEVKVNIEQGHAILAGHSFEHELALANALGIFGSIDMNRND 300
           QYDYDVATVYGFLK++GLENEVK+NIEQGHAILAGHSFEHELALANALGIFGSIDMNRND
Sbjct: 241 QYDYDVATVYGFLKKHGLENEVKLNIEQGHAILAGHSFEHELALANALGIFGSIDMNRND 300

Query: 301 YQSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDAKLRRQSIDPEDLLIGHIGGMD 360
           YQSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFD+KLRRQS+DP DLLIGHIGGMD
Sbjct: 301 YQSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDSKLRRQSLDPADLLIGHIGGMD 360

Query: 361 CCARGLKAAAKMIEDKALSAPLEARYAGWNVPEAKKMLDGGFSLEEIEAWVLKSDVNPQP 420
           CCARGLKAAAKMIEDKALS PL  RYAGW   EA+K+  G +SL+EI  +V   DVNPQP
Sbjct: 361 CCARGLKAAAKMIEDKALSQPLADRYAGWESAEAQKLFRGEYSLDEITHYVESHDVNPQP 420

Query: 421 KSGRQELLENVVNRYV 436
           +SG+QELLENVVNRYV
Sbjct: 421 RSGKQELLENVVNRYV 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: 855
Number of extensions: 29
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 WP_003552938.1 RL_RS21535 (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.5142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-214  697.4   0.0   4.2e-214  697.3   0.0    1.0  1  lcl|NCBI__GCF_000009265.1:WP_003552938.1  RL_RS21535 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_003552938.1  RL_RS21535 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  697.3   0.0  4.2e-214  4.2e-214       1     435 []       5     436 .]       5     436 .] 1.00

  Alignments for each domain:
  == domain 1  score: 697.3 bits;  conditional E-value: 4.2e-214
                                 TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdke 69 
                                               ff +i+kvkyeG+ds+nplaf++y+p+e+++gk+m+dhlrfavayWht+++ g+DpfG++t+ rpw   
  lcl|NCBI__GCF_000009265.1:WP_003552938.1   5 FFGDIQKVKYEGPDSTNPLAFRHYQPDEIVMGKRMEDHLRFAVAYWHTFTWPGGDPFGGQTFLRPWF-- 71 
                                               799***************************************************************9.. PP

                                 TIGR02630  70 ltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWg 138
                                                +d++++ak k+d+afe+++ lg +yycfhD+D+ peg++++e+++nl+eivd++ ekq++tg klLWg
  lcl|NCBI__GCF_000009265.1:WP_003552938.1  72 -EDTMKAAKLKADVAFEFFSLLGSPYYCFHDADVRPEGKTFAENTKNLNEIVDYFAEKQAATGTKLLWG 139
                                               .589***************************************************************** PP

                                 TIGR02630 139 tanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnl 207
                                               tanlfsh+ry+ Gaat+pd+dvfa+aaa+vk+++++t+klggenyv+WGGreGyetLlntd+ +eld+l
  lcl|NCBI__GCF_000009265.1:WP_003552938.1 140 TANLFSHRRYMSGAATNPDPDVFAFAAATVKTCIDATQKLGGENYVLWGGREGYETLLNTDIGRELDQL 208
                                               ********************************************************************* PP

                                 TIGR02630 208 arflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaght 276
                                               +rfl+l+v+y++kig+kg++liePkP+ePtkhqyD+D+atv++flkk++L++++klnie+ ha+Lagh+
  lcl|NCBI__GCF_000009265.1:WP_003552938.1 209 GRFLNLVVEYKHKIGYKGTILIEPKPQEPTKHQYDYDVATVYGFLKKHGLENEVKLNIEQGHAILAGHS 277
                                               ********************************************************************* PP

                                 TIGR02630 277 fehelrvarelgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresl 345
                                               fehel++a++lg++GsiD+nr+d++ GWDtD+fp++v e++la+y+vl  gg+++GG+nfd+k+rr+sl
  lcl|NCBI__GCF_000009265.1:WP_003552938.1 278 FEHELALANALGIFGSIDMNRNDYQSGWDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDSKLRRQSL 346
                                               ********************************************************************* PP

                                 TIGR02630 346 daeDlllahiagmDafarglkvaaklledgaleklveeryesfdseiGkeieegkadleelekyaleke 414
                                               d+ Dll++hi+gmD++arglk+aak++ed+al++ +++ry++++s   +++  g+ +l+e+++y+++++
  lcl|NCBI__GCF_000009265.1:WP_003552938.1 347 DPADLLIGHIGGMDCCARGLKAAAKMIEDKALSQPLADRYAGWESAEAQKLFRGEYSLDEITHYVESHD 415
                                               ********************************************************************* PP

                                 TIGR02630 415 eeaekksgrqelleslinkyl 435
                                                +++ +sg+qelle+++n+y+
  lcl|NCBI__GCF_000009265.1:WP_003552938.1 416 VNPQPRSGKQELLENVVNRYV 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: 10.74
//
[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:

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