Alignments for a candidate for xylB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Phaeobacter inhibens BS107

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate GFF1384 PGA1_c14010 xylulose kinase XylB

Query= reanno::Phaeo:GFF1384
         (478 letters)



>FitnessBrowser__Phaeo:GFF1384
          Length = 478

 Score =  972 bits (2513), Expect = 0.0
 Identities = 478/478 (100%), Positives = 478/478 (100%)

Query: 1   MYLGIDLGTSGLRALMTDAAGKPVASAEAQYDVQTPHPGWSEQDPGDWITALDQAMAQLQ 60
           MYLGIDLGTSGLRALMTDAAGKPVASAEAQYDVQTPHPGWSEQDPGDWITALDQAMAQLQ
Sbjct: 1   MYLGIDLGTSGLRALMTDAAGKPVASAEAQYDVQTPHPGWSEQDPGDWITALDQAMAQLQ 60

Query: 61  GSPGYSDICGIAVAGHMHGAVLLDGSDQVLRPCILWNDTRSAAEAAELDAAEKVRDLSGN 120
           GSPGYSDICGIAVAGHMHGAVLLDGSDQVLRPCILWNDTRSAAEAAELDAAEKVRDLSGN
Sbjct: 61  GSPGYSDICGIAVAGHMHGAVLLDGSDQVLRPCILWNDTRSAAEAAELDAAEKVRDLSGN 120

Query: 121 IVFPGFTAPKLLWVQRHEPEIFANTAKVLLPAAYLNLHLTGRHVADMSDSAGTSWLDVGA 180
           IVFPGFTAPKLLWVQRHEPEIFANTAKVLLPAAYLNLHLTGRHVADMSDSAGTSWLDVGA
Sbjct: 121 IVFPGFTAPKLLWVQRHEPEIFANTAKVLLPAAYLNLHLTGRHVADMSDSAGTSWLDVGA 180

Query: 181 RDWSEWLLEAGHMRRDQMPDLVEGSAAAGTLRPELAVRWGLTGPVTIAGGAGDNAAAACG 240
           RDWSEWLLEAGHMRRDQMPDLVEGSAAAGTLRPELAVRWGLTGPVTIAGGAGDNAAAACG
Sbjct: 181 RDWSEWLLEAGHMRRDQMPDLVEGSAAAGTLRPELAVRWGLTGPVTIAGGAGDNAAAACG 240

Query: 241 TGVMAPGQGFVSLGTSGVVLTARDGFRPDPATAVHTFCHAIPDRWYQMGVMLSATDCMNW 300
           TGVMAPGQGFVSLGTSGVVLTARDGFRPDPATAVHTFCHAIPDRWYQMGVMLSATDCMNW
Sbjct: 241 TGVMAPGQGFVSLGTSGVVLTARDGFRPDPATAVHTFCHAIPDRWYQMGVMLSATDCMNW 300

Query: 301 LGRITGQSPADLTAGLGEELQPPGPVTFMPYLSGERTPHNSASLRGGFQGLSIATTAEDL 360
           LGRITGQSPADLTAGLGEELQPPGPVTFMPYLSGERTPHNSASLRGGFQGLSIATTAEDL
Sbjct: 301 LGRITGQSPADLTAGLGEELQPPGPVTFMPYLSGERTPHNSASLRGGFQGLSIATTAEDL 360

Query: 361 ARAVMEGVCYGLRDCLEALRKTGAEIDSCLVIGGGSKSAYWVKLLATILDLPLQLPKDGE 420
           ARAVMEGVCYGLRDCLEALRKTGAEIDSCLVIGGGSKSAYWVKLLATILDLPLQLPKDGE
Sbjct: 361 ARAVMEGVCYGLRDCLEALRKTGAEIDSCLVIGGGSKSAYWVKLLATILDLPLQLPKDGE 420

Query: 421 FGAALGAARLARLAVTGDDPADVLTAPESAMTVAPDPLLRDGYEAGYAAFRRRGAELT 478
           FGAALGAARLARLAVTGDDPADVLTAPESAMTVAPDPLLRDGYEAGYAAFRRRGAELT
Sbjct: 421 FGAALGAARLARLAVTGDDPADVLTAPESAMTVAPDPLLRDGYEAGYAAFRRRGAELT 478


Lambda     K      H
   0.318    0.135    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: 1052
Number of extensions: 48
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF1384 PGA1_c14010 (xylulose kinase XylB)
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

# 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/TIGR01312.hmm
# target sequence database:        /tmp/gapView.14325.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01312  [M=481]
Accession:   TIGR01312
Description: XylB: xylulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     8e-165  534.9   0.0   9.4e-165  534.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1384  PGA1_c14010 xylulose kinase XylB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1384  PGA1_c14010 xylulose kinase XylB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.7   0.0  9.4e-165  9.4e-165       1     473 [.       3     467 ..       3     473 .. 0.96

  Alignments for each domain:
  == domain 1  score: 534.7 bits;  conditional E-value: 9.4e-165
                          TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQ 76 
                                        lGiDlgTs+++al+ d+ g+ +as++a+++v++p+pgwsEqdp +w+ al++a+++l+ +     ++i +i+++G 
  lcl|FitnessBrowser__Phaeo:GFF1384   3 LGIDLGTSGLRALMTDAAGKPVASAEAQYDVQTPHPGWSEQDPGDWITALDQAMAQLQGSPG--YSDICGIAVAGH 76 
                                        7********************************************************99977..69********** PP

                          TIGR01312  77 mHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariakvl 152
                                        mHg+vlLD +++vlrp+iLWnDtr+a+e++el+++   e++++l gn++++gfTapKllWv++hepe+fa++akvl
  lcl|FitnessBrowser__Phaeo:GFF1384  77 MHGAVLLDGSDQVLRPCILWNDTRSAAEAAELDAA---EKVRDLSGNIVFPGFTAPKLLWVQRHEPEIFANTAKVL 149
                                        ********************************986...58************************************ PP

                          TIGR01312 153 LPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGleegv 228
                                        LP  yl+++Ltg++v+++sD++GT ++dv  r+ws+ ll+a ++ ++++P lve+s+ aG++r+e+a ++Gl   v
  lcl|FitnessBrowser__Phaeo:GFF1384 150 LPAAYLNLHLTGRHVADMSDSAGTSWLDVGARDWSEWLLEAGHMRRDQMPDLVEGSAAAGTLRPELAVRWGLTGPV 225
                                        **************************************************************************** PP

                          TIGR01312 229 kvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewl 304
                                        ++a+G+gdnaa+A+G+g++++g+ +vslGtSGvvl++ d  ++dp++avh+Fcha p++wy++gv+lsat++++wl
  lcl|FitnessBrowser__Phaeo:GFF1384 226 TIAGGAGDNAAAACGTGVMAPGQGFVSLGTSGVVLTARDGFRPDPATAVHTFCHAIPDRWYQMGVMLSATDCMNWL 301
                                        **************************************************************************** PP

                          TIGR01312 305 kellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradlarAvlegvafalrdsl 380
                                         +++g++  + ++ + e+ ++   +v+++PylsGERtPh+ ++ rg + Gl+ +tt +dlarAv+egv ++lrd l
  lcl|FitnessBrowser__Phaeo:GFF1384 302 GRITGQSPADLTAGLGEELQPP-GPVTFMPYLSGERTPHNSASLRGGFQGLSIATTAEDLARAVMEGVCYGLRDCL 376
                                        *****99998888999999988.9**************************************************** PP

                          TIGR01312 381 dilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseavvkq 455
                                        ++l++ +g +i+++ +iGGG+ks++w ++la+il+l+++ p+  e gaalGaA+lA +a + +d ++++++  ++ 
  lcl|FitnessBrowser__Phaeo:GFF1384 377 EALRK-TGAEIDSCLVIGGGSKSAYWVKLLATILDLPLQLPKdGEFGAALGAARLARLAVTGDDPADVLTAPESAM 451
                                        *****.77**********************************999****************999999988877665 PP

                          TIGR01312 456 kesvepiaenveayeely 473
                                        +    p+      ye  y
  lcl|FitnessBrowser__Phaeo:GFF1384 452 TVA--PDPLLRDGYEAGY 467
                                        544..5555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (478 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: 11.86
//
[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