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.620155.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.49
//
[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:

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