Alignments for a candidate for xylG in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Pseudomonas simiae WCS417

Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein

Query= SwissProt::P37388
         (513 letters)



>FitnessBrowser__WCS417:GFF2162
          Length = 500

 Score =  348 bits (892), Expect = e-100
 Identities = 199/500 (39%), Positives = 313/500 (62%), Gaps = 13/500 (2%)

Query: 5   LEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEII 64
           L    I KTF  VKA+D +    + G++ +L GENG+GKSTL+K+L G Y   S     +
Sbjct: 6   LRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNS---GTL 62

Query: 65  FAGEEIQA-SHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLRC 123
             GE++ A     D+   G+A+IHQEL LV E++V EN+FLG+  +  G+++  L+  + 
Sbjct: 63  HIGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRKQA 122

Query: 124 QKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLD 183
              L  ++  I P  ++G L LGQ+QLVEIAKAL++   ++  DEPT+SL+ +E   L+ 
Sbjct: 123 LACLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMA 182

Query: 184 IIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGT-RDAAGMSEDDIITMMVGRE 242
           II  L+  G   +Y+SH++ EV  I + + V +DG+++ T  D + ++ D ++T MVGR+
Sbjct: 183 IIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVGRD 242

Query: 243 LTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTE 302
           +  +Y   P   G+  L+++ L    P  R       VSF++++GEILG+ GLVGAGRTE
Sbjct: 243 IQDIYDYRPREHGEVALKVDGLLG--PGLRE-----PVSFNVRKGEILGLFGLVGAGRTE 295

Query: 303 TIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNIT 362
             + L G+      G++ + G+ + +++ + AIA G+ + PEDRK++GI+P+ +V +NI 
Sbjct: 296 LFRLLSGLERAS-AGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENIN 354

Query: 363 LAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLLL 422
           ++A    +     L +  E+    + I  +KVKT +    I  LSGGNQQK+IL R L +
Sbjct: 355 ISARGAHSTFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSM 414

Query: 423 NPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEGK 482
             ++L+LDEPTRGIDIGAK EIY++I+ L  QGIAVIV+SS+L EV+G++DR+LV+ EG 
Sbjct: 415 PMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGA 474

Query: 483 LKANLINHNLTQEQVMEAAL 502
           L+      + T+  +++ AL
Sbjct: 475 LRGEQTREHATESNLLQLAL 494



 Score = 63.2 bits (152), Expect = 2e-14
 Identities = 54/228 (23%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 23  VCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEEIQASHIRDTERKG 82
           V   +  GEI+ L G  G+G++ L ++L G+    +  G++   GE +     RD    G
Sbjct: 273 VSFNVRKGEILGLFGLVGAGRTELFRLLSGL--ERASAGQLELCGEPLHLQSPRDAIAAG 330

Query: 83  IAIIHQEL---ALVKELTVLENIFLGNEITHNG----IMDYDLMTLRCQKLLAQVSLSIS 135
           + +  ++     ++   +V ENI +     H+     + +        Q++ A    + +
Sbjct: 331 VLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLREGWEKGNADQQINAMKVKTPN 390

Query: 136 PDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQHGIAC 195
              ++  L  G QQ   + + L+  +++L+LDEPT  +     + +  II +L   GIA 
Sbjct: 391 AAQKIMYLSGGNQQKSILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAQGIAV 450

Query: 196 IYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGREL 243
           I +S  L EV  I+D I V+ +G   G +     +E +++ + + R +
Sbjct: 451 IVVSSDLMEVMGIADRILVLCEGALRGEQTREHATESNLLQLALPRSV 498


Lambda     K      H
   0.319    0.137    0.391 

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: 621
Number of extensions: 30
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 513
Length of database: 500
Length adjustment: 34
Effective length of query: 479
Effective length of database: 466
Effective search space:   223214
Effective search space used:   223214
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: 52 (24.6 bits)

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