Alignments for a candidate for xylA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Klebsiella michiganensis M5al

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate BWI76_RS27025 BWI76_RS27025 xylose isomerase

Query= reanno::Koxy:BWI76_RS27025
         (440 letters)



>FitnessBrowser__Koxy:BWI76_RS27025
          Length = 440

 Score =  915 bits (2366), Expect = 0.0
 Identities = 440/440 (100%), Positives = 440/440 (100%)

Query: 1   MQTYFDQLDRVRYEGPKSANPLAFRHYNPDELVLGKRMEDHLRFAACYWHTFCWNGADMF 60
           MQTYFDQLDRVRYEGPKSANPLAFRHYNPDELVLGKRMEDHLRFAACYWHTFCWNGADMF
Sbjct: 1   MQTYFDQLDRVRYEGPKSANPLAFRHYNPDELVLGKRMEDHLRFAACYWHTFCWNGADMF 60

Query: 61  GVGSFNRPWQQPGEAMEMAKRKADVAFEFFHKLNVPYYCFHDVDVSPEGASLKEYANNFA 120
           GVGSFNRPWQQPGEAMEMAKRKADVAFEFFHKLNVPYYCFHDVDVSPEGASLKEYANNFA
Sbjct: 61  GVGSFNRPWQQPGEAMEMAKRKADVAFEFFHKLNVPYYCFHDVDVSPEGASLKEYANNFA 120

Query: 121 QMVDVLAEKQQQSGVKLLWGTANCFTNPRYGAGAATNPDPEVFSWAATQVVTAMDATHKL 180
           QMVDVLAEKQQQSGVKLLWGTANCFTNPRYGAGAATNPDPEVFSWAATQVVTAMDATHKL
Sbjct: 121 QMVDVLAEKQQQSGVKLLWGTANCFTNPRYGAGAATNPDPEVFSWAATQVVTAMDATHKL 180

Query: 181 GGENYVLWGGREGYETLLNTDLRQEREQIGRFMQLVVEHKHKIGFQGTLLIEPKPQEPTK 240
           GGENYVLWGGREGYETLLNTDLRQEREQIGRFMQLVVEHKHKIGFQGTLLIEPKPQEPTK
Sbjct: 181 GGENYVLWGGREGYETLLNTDLRQEREQIGRFMQLVVEHKHKIGFQGTLLIEPKPQEPTK 240

Query: 241 HQYDYDASTVYGFLKQFGLEKEIKLNIEANHATLAGHTFHHEIATAIALGLFGSVDANRG 300
           HQYDYDASTVYGFLKQFGLEKEIKLNIEANHATLAGHTFHHEIATAIALGLFGSVDANRG
Sbjct: 241 HQYDYDASTVYGFLKQFGLEKEIKLNIEANHATLAGHTFHHEIATAIALGLFGSVDANRG 300

Query: 301 DPQLGWDTDQFPNSVEENALVMYEILKAGGFTTGGLNFDAKVRRQSTDKYDLFYGHIGAM 360
           DPQLGWDTDQFPNSVEENALVMYEILKAGGFTTGGLNFDAKVRRQSTDKYDLFYGHIGAM
Sbjct: 301 DPQLGWDTDQFPNSVEENALVMYEILKAGGFTTGGLNFDAKVRRQSTDKYDLFYGHIGAM 360

Query: 361 DTMALALKVAARMIEGGELDKRVAKRYAGWNGELGQQILKGQMNLADIAQYATQHNLAPQ 420
           DTMALALKVAARMIEGGELDKRVAKRYAGWNGELGQQILKGQMNLADIAQYATQHNLAPQ
Sbjct: 361 DTMALALKVAARMIEGGELDKRVAKRYAGWNGELGQQILKGQMNLADIAQYATQHNLAPQ 420

Query: 421 HQSGHQELLENVVNRYLFDR 440
           HQSGHQELLENVVNRYLFDR
Sbjct: 421 HQSGHQELLENVVNRYLFDR 440


Lambda     K      H
   0.320    0.136    0.419 

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: 904
Number of extensions: 21
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: 440
Length of database: 440
Length adjustment: 32
Effective length of query: 408
Effective length of database: 408
Effective search space:   166464
Effective search space used:   166464
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 BWI76_RS27025 BWI76_RS27025 (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.5677.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.5e-223  728.4   1.1   1.7e-223  728.2   1.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27025  BWI76_RS27025 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27025  BWI76_RS27025 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  728.2   1.1  1.7e-223  1.7e-223       1     435 []       4     437 ..       4     437 .. 1.00

  Alignments for each domain:
  == domain 1  score: 728.2 bits;  conditional E-value: 1.7e-223
                               TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkelt 71 
                                             +f+++++v+yeG++s nplaf++ynp+e++ gk+m+dhlrfa +yWht++++gaD+fG g+++rpw++   
  lcl|FitnessBrowser__Koxy:BWI76_RS27025   4 YFDQLDRVRYEGPKSANPLAFRHYNPDELVLGKRMEDHLRFAACYWHTFCWNGADMFGVGSFNRPWQQP-G 73 
                                             8*****************************************************************965.9 PP

                               TIGR02630  72 daldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanl 142
                                             +a+++ak+k+d+afe+++kl+v+yycfhDvD++pegaslke+ +n+ ++vd+l ekq+++gvklLWgtan+
  lcl|FitnessBrowser__Koxy:BWI76_RS27025  74 EAMEMAKRKADVAFEFFHKLNVPYYCFHDVDVSPEGASLKEYANNFAQMVDVLAEKQQQSGVKLLWGTANC 144
                                             *********************************************************************** PP

                               TIGR02630 143 fshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflkl 213
                                             f++pry aGaat+pd++vf++aa+qv +a+++t+klggenyv+WGGreGyetLlntdl++e+++++rf++l
  lcl|FitnessBrowser__Koxy:BWI76_RS27025 145 FTNPRYGAGAATNPDPEVFSWAATQVVTAMDATHKLGGENYVLWGGREGYETLLNTDLRQEREQIGRFMQL 215
                                             *********************************************************************** PP

                               TIGR02630 214 avdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrva 284
                                             +v++++kigf+g+lliePkP+ePtkhqyD+Da+tv++flk+++L+k++klnieanhatLaghtf+he+++a
  lcl|FitnessBrowser__Koxy:BWI76_RS27025 216 VVEHKHKIGFQGTLLIEPKPQEPTKHQYDYDASTVYGFLKQFGLEKEIKLNIEANHATLAGHTFHHEIATA 286
                                             *********************************************************************** PP

                               TIGR02630 285 relgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahi 355
                                              +lgl+Gs+Danrgd +lGWDtD+fp++v+e++l+mye+lkagg+++GGlnfdakvrr+s+d+ Dl+++hi
  lcl|FitnessBrowser__Koxy:BWI76_RS27025 287 IALGLFGSVDANRGDPQLGWDTDQFPNSVEENALVMYEILKAGGFTTGGLNFDAKVRRQSTDKYDLFYGHI 357
                                             *********************************************************************** PP

                               TIGR02630 356 agmDafarglkvaaklledgaleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqel 426
                                             ++mD++a++lkvaa+++e g+l+k v++ry++++ e+G++i++g+++l+++++ya++++ +++++sg+qel
  lcl|FitnessBrowser__Koxy:BWI76_RS27025 358 GAMDTMALALKVAARMIEGGELDKRVAKRYAGWNGELGQQILKGQMNLADIAQYATQHNLAPQHQSGHQEL 428
                                             *********************************************************************** PP

                               TIGR02630 427 leslinkyl 435
                                             le+++n+yl
  lcl|FitnessBrowser__Koxy:BWI76_RS27025 429 LENVVNRYL 437
                                             *******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (440 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: 10.60
//
[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