GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylG in Pseudomonas fluorescens FW300-N2C3

Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate AO356_28510 AO356_28510 xylose transporter

Query= SwissProt::P37388
         (513 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28510
          Length = 518

 Score =  550 bits (1418), Expect = e-161
 Identities = 280/502 (55%), Positives = 374/502 (74%), Gaps = 3/502 (0%)

Query: 3   YLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGE 62
           YLL+M  I KTFG VKA++ + +++  GE V LCGENG+GKSTLMKVL  +YPHG++EGE
Sbjct: 4   YLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPHGTWEGE 63

Query: 63  IIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEIT-HNGIMDYDLMTL 121
           II+ G+ ++A  I +TE  GI IIHQEL LV +L+V ENIF+G+E+T   G M+Y  M  
Sbjct: 64  IIWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIH 123

Query: 122 RCQKLLAQVSL-SISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSI 180
           R + L+ ++ +  ++    V   G G QQLVEIAKALNKQ RLLILDEP+++LT  E  +
Sbjct: 124 RAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEV 183

Query: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVG 240
           LLDIIRDL+  G+AC+YISHKL+EV A+ DTI VIRDG+HI T     M    IIT MVG
Sbjct: 184 LLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMTDMDIPKIITQMVG 243

Query: 241 RELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGR 300
           RE++ LYP EPH  G+ I    H+T +   N   KRV+D+SF LKRGEILGIAGLVGAGR
Sbjct: 244 REMSNLYPTEPHDIGEVIFEARHVTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAGR 303

Query: 301 TETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360
           TE +  LFG +PG++EG+++++G+Q+D R   ++I  G+ MVPEDRKR GI+P + VG+N
Sbjct: 304 TELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQN 363

Query: 361 ITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCL 420
           ITLA L+ ++  ++++D  AE   I + I ++ +KT+SP L I  LSGGNQQKA+LA+ L
Sbjct: 364 ITLAVLDNYS-KLTRIDAEAELGSIDKEIARMHLKTASPFLPITSLSGGNQQKAVLAKML 422

Query: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480
           L  PR+LILDEPTRG+D+GAKYEIYKL+  L  +G+++I++SSEL EVLG+SDRVLV+ +
Sbjct: 423 LTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIGD 482

Query: 481 GKLKANLINHNLTQEQVMEAAL 502
           G+L+ + INH LTQEQV+ AAL
Sbjct: 483 GQLRGDFINHELTQEQVLAAAL 504


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: 787
Number of extensions: 33
Number of successful extensions: 9
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: 513
Length of database: 518
Length adjustment: 35
Effective length of query: 478
Effective length of database: 483
Effective search space:   230874
Effective search space used:   230874
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:

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