Alignments for a candidate for xylA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Phaeobacter inhibens BS107

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate GFF1383 PGA1_c14000 xylose isomerase XylA

Query= reanno::Phaeo:GFF1383
         (434 letters)



>FitnessBrowser__Phaeo:GFF1383
          Length = 434

 Score =  895 bits (2314), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MAGYFDDIAAITYNPESDRLAYRHYNPDEMIMGKRMEDHLRFAVCYWHNFVWEGNDPFGG 60
           MAGYFDDIAAITYNPESDRLAYRHYNPDEMIMGKRMEDHLRFAVCYWHNFVWEGNDPFGG
Sbjct: 1   MAGYFDDIAAITYNPESDRLAYRHYNPDEMIMGKRMEDHLRFAVCYWHNFVWEGNDPFGG 60

Query: 61  QTFQRPWFPADTMDLARMKADAAFDMFRILGVPYYCFHDHDIRPEGASLAESHKRLNQIG 120
           QTFQRPWFPADTMDLARMKADAAFDMFRILGVPYYCFHDHDIRPEGASLAESHKRLNQIG
Sbjct: 61  QTFQRPWFPADTMDLARMKADAAFDMFRILGVPYYCFHDHDIRPEGASLAESHKRLNQIG 120

Query: 121 DLLEQKMADGGPKLLWGTANMFSNRRYMSGASTNPDPDVFAYCASTVRACMDLTHRLNGE 180
           DLLEQKMADGGPKLLWGTANMFSNRRYMSGASTNPDPDVFAYCASTVRACMDLTHRLNGE
Sbjct: 121 DLLEQKMADGGPKLLWGTANMFSNRRYMSGASTNPDPDVFAYCASTVRACMDLTHRLNGE 180

Query: 181 NYVLWGGREGYETLLNTDLSRELEQMGRFLSMVVDYKHKIGFMGAILIEPKPQEPTKHQY 240
           NYVLWGGREGYETLLNTDLSRELEQMGRFLSMVVDYKHKIGFMGAILIEPKPQEPTKHQY
Sbjct: 181 NYVLWGGREGYETLLNTDLSRELEQMGRFLSMVVDYKHKIGFMGAILIEPKPQEPTKHQY 240

Query: 241 DYDVATVYGFLKRFGLEEEVKVNIEQGHAILAGHSFEHEIAMANALGIFGSIDMNRNDYQ 300
           DYDVATVYGFLKRFGLEEEVKVNIEQGHAILAGHSFEHEIAMANALGIFGSIDMNRNDYQ
Sbjct: 241 DYDVATVYGFLKRFGLEEEVKVNIEQGHAILAGHSFEHEIAMANALGIFGSIDMNRNDYQ 300

Query: 301 SGWDTDQFPNNVPEVALAYYEILRGGGLKTGGTNFDAKLRRQSLDAEDLIAAHVGAMDVC 360
           SGWDTDQFPNNVPEVALAYYEILRGGGLKTGGTNFDAKLRRQSLDAEDLIAAHVGAMDVC
Sbjct: 301 SGWDTDQFPNNVPEVALAYYEILRGGGLKTGGTNFDAKLRRQSLDAEDLIAAHVGAMDVC 360

Query: 361 ARGLRAAAAMLESDSLEAKRRDRYAGWTTAEAQAYLAEGATLEAIADQAEARALNPQPVS 420
           ARGLRAAAAMLESDSLEAKRRDRYAGWTTAEAQAYLAEGATLEAIADQAEARALNPQPVS
Sbjct: 361 ARGLRAAAAMLESDSLEAKRRDRYAGWTTAEAQAYLAEGATLEAIADQAEARALNPQPVS 420

Query: 421 GRQEQLEALVNRFV 434
           GRQEQLEALVNRFV
Sbjct: 421 GRQEQLEALVNRFV 434


Lambda     K      H
   0.320    0.136    0.418 

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: 860
Number of extensions: 19
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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 GFF1383 PGA1_c14000 (xylose isomerase XylA)
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.23327.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.1e-199  648.8   0.0   2.3e-199  648.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1383  PGA1_c14000 xylose isomerase Xyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1383  PGA1_c14000 xylose isomerase XylA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.7   0.0  2.3e-199  2.3e-199       1     435 []       4     434 .]       4     434 .] 0.99

  Alignments for each domain:
  == domain 1  score: 648.7 bits;  conditional E-value: 2.3e-199
                          TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltdaldk 76 
                                        +f++i+ ++y+ +  ++ la+++ynp+e+i+gk+m+dhlrfav+yWh + +eg+DpfG++t++rpw    +d++d 
  lcl|FitnessBrowser__Phaeo:GFF1383   4 YFDDIAAITYNPE--SDRLAYRHYNPDEMIMGKRMEDHLRFAVCYWHNFVWEGNDPFGGQTFQRPWFP--ADTMDL 75 
                                        89********854..578************************************************94..79**** PP

                          TIGR02630  77 akakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshpryvaGa 152
                                        a+ k+daaf++++ lgv+yycfhD Di pegasl+e+++ l++i dll++k+++ g klLWgtan+fs++ry+ Ga
  lcl|FitnessBrowser__Phaeo:GFF1383  76 ARMKADAAFDMFRILGVPYYCFHDHDIRPEGASLAESHKRLNQIGDLLEQKMADGGPKLLWGTANMFSNRRYMSGA 151
                                        **************************************************************************** PP

                          TIGR02630 153 atspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyakkigfkgqll 228
                                        +t+pd+dvfay+a++v++++++t++l+genyv+WGGreGyetLlntdl++el++++rfl+++vdy++kigf g +l
  lcl|FitnessBrowser__Phaeo:GFF1383 152 STNPDPDVFAYCASTVRACMDLTHRLNGENYVLWGGREGYETLLNTDLSRELEQMGRFLSMVVDYKHKIGFMGAIL 227
                                        **************************************************************************** PP

                          TIGR02630 229 iePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGsiDanrgdlllGW 304
                                        iePkP+ePtkhqyD+D+atv++flk+++L++++k+nie+ ha+Lagh+fehe+++a++lg++GsiD+nr+d++ GW
  lcl|FitnessBrowser__Phaeo:GFF1383 228 IEPKPQEPTKHQYDYDVATVYGFLKRFGLEEEVKVNIEQGHAILAGHSFEHEIAMANALGIFGSIDMNRNDYQSGW 303
                                        **************************************************************************** PP

                          TIGR02630 305 DtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledgalekl 380
                                        DtD+fp++v e++la+ye+l+ ggl++GG+nfdak+rr+sldaeDl+ ah+++mD +argl++aa++le+++le+ 
  lcl|FitnessBrowser__Phaeo:GFF1383 304 DTDQFPNNVPEVALAYYEILRGGGLKTGGTNFDAKLRRQSLDAEDLIAAHVGAMDVCARGLRAAAAMLESDSLEAK 379
                                        **************************************************************************** PP

                          TIGR02630 381 veeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                         ++ry+++++   ++ ++  a+le ++++a+ +  +++  sgrqe+le+l+n+++
  lcl|FitnessBrowser__Phaeo:GFF1383 380 RRDRYAGWTTAEAQAYLAEGATLEAIADQAEARALNPQPVSGRQEQLEALVNRFV 434
                                        **********9999999999********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (434 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.94
//
[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