Alignments for a candidate for xylG in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Echinicola vietnamensis KMM 6221, DSM 17526

Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= SwissProt::P37388
         (513 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  425 bits (1093), Expect = e-123
 Identities = 232/501 (46%), Positives = 339/501 (67%), Gaps = 6/501 (1%)

Query: 4   LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63
           +L +KNITK F  VKA+D+V L L AG + ++ GENG+GKSTLMK+L G+YP   Y+G I
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYP--DYKGTI 58

Query: 64  IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEI-THNGIMDYDLMTLR 122
            + G+ ++  + RD + KGI IIHQEL L+  L++ ENIFLG E  T  G++D   M   
Sbjct: 59  YYNGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKE 118

Query: 123 CQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILL 182
             +LL ++ L++ P+T V  L +GQQQLVEIAKAL+ + +++I+DEPT+++++QE  IL 
Sbjct: 119 AAQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILF 178

Query: 183 DIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGRE 242
            IIR L+  G A  YISHKL+E+ AI+D   V+RDG+ I + +  GM+E+ +I  MVGRE
Sbjct: 179 GIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGRE 238

Query: 243 LTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTE 302
           +            + +L ++HLT  HP       + D++F L +GE+LGI GL+GAGRTE
Sbjct: 239 IVIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTE 298

Query: 303 TIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNIT 362
            ++ LFGV P Q   +I + GK  + +  Q+A+  G+A+VPEDRK+DG+V  M +  N +
Sbjct: 299 LMEALFGVLPHQG-AEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSS 357

Query: 363 LAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLLL 422
           L  ++    G   LDD  E+    + + +LK+K SS    + +LSGGNQQK +LA+ L  
Sbjct: 358 LTVVDSILSG-GLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLAT 416

Query: 423 NPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEGK 482
            P++L+LDEPTRGIDI AK EIYKLI QL  +G+ +IV+SSELPE+L +SDRVLVM EG+
Sbjct: 417 RPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGR 476

Query: 483 LKANL-INHNLTQEQVMEAAL 502
           L AN+ I+   +++++++AA+
Sbjct: 477 LTANIPIDAQTSEDEILQAAI 497



 Score =  103 bits (258), Expect = 1e-26
 Identities = 66/237 (27%), Positives = 129/237 (54%), Gaps = 7/237 (2%)

Query: 274 IKRVNDVSFSLKRGEILGIAGLVGAGRTETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQ 333
           +K ++DVS  L+ G +  I G  GAG++  ++ L GV+P  ++G IY +G  V  +N + 
Sbjct: 14  VKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYP-DYKGTIYYNGDPVKFQNTRD 72

Query: 334 AIAQGIAMVPEDRKRDGIVPVMAVGKNITLAALNKFTGGISQLDDAAEQKCILESIQQLK 393
           A  +GI ++ ++     ++P +++ +NI L    +   G+  LD A   K   + + +LK
Sbjct: 73  AQEKGINIIHQELN---LIPYLSIRENIFLGREPETPMGL--LDVAKMHKEAAQLLHRLK 127

Query: 394 VKTSSPDLAIGRLSGGNQQKAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQ 453
           +    P+  + +L  G QQ   +A+ L L  +++I+DEPT  I       ++ +I  L  
Sbjct: 128 LNVD-PETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALRA 186

Query: 454 QGIAVIVISSELPEVLGLSDRVLVMHEGKLKANLINHNLTQEQVMEAALRSEHHVEK 510
           +G A+  IS +L E+  ++DR +V+ +GK+  +     +T+E +++  +  E  +E+
Sbjct: 187 EGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREIVIER 243


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: 678
Number of extensions: 37
Number of successful extensions: 11
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: 502
Length adjustment: 34
Effective length of query: 479
Effective length of database: 468
Effective search space:   224172
Effective search space used:   224172
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