GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Sinorhizobium meliloti 1021

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate SMc02031 SMc02031 permease

Query= TCDB::Q9WXW7
         (317 letters)



>FitnessBrowser__Smeli:SMc02031
          Length = 349

 Score =  226 bits (575), Expect = 8e-64
 Identities = 130/327 (39%), Positives = 191/327 (58%), Gaps = 19/327 (5%)

Query: 3   SKFKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIIS 62
           +K K   F + GPL+ALV L  + A     FLT  NL  + RQ A   +LA+G+TFVI++
Sbjct: 21  TKLKAVVF-QAGPLIALVLLMAYLAFATSNFLTLDNLSNVARQSAFVAILAVGQTFVILT 79

Query: 63  GGGAIDLSPGSMVALTGVMVAWLMTHG----------VPVWISVILILLFSIGAGAWHGL 112
           GG  IDLS  ++ AL+  + A L+T            VP  +++++ +L  + AGA +G 
Sbjct: 80  GG--IDLSVAAIAALSASITAVLLTQPLVLFGIDFGFVPPPVAILIGILIGMAAGALNGW 137

Query: 113 FVTKLRVPAFIITLGTLTIARGMAAVITKGWPIIG------LPSSFLKIGQGEFLKIPIP 166
            ++K ++P FI TLGT+T  RG A ++T G P+        LP S + +G G+   +P+ 
Sbjct: 138 LISKFKIPDFIATLGTMTAFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLFGVPVS 197

Query: 167 VWILLAVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVG 226
             I L  A    + LR T  G+ + A GGN  AA  SG+++ R +++ + +SG LA + G
Sbjct: 198 ALIALLCAAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAG 257

Query: 227 IIIAARLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLL 286
           II+  RL+     +    EL +IAS VIGGT+L GGEG V G+I+GA+II +L N L LL
Sbjct: 258 IILVGRLNSANALMADGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLL 317

Query: 287 NVSTYWHNVVIGIVIVVAVTLDILRRR 313
           +VS +W  +  G+VIVV V  D  RRR
Sbjct: 318 DVSPFWQRIAQGVVIVVVVIFDQWRRR 344


Lambda     K      H
   0.328    0.143    0.424 

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: 372
Number of extensions: 22
Number of successful extensions: 4
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: 317
Length of database: 349
Length adjustment: 28
Effective length of query: 289
Effective length of database: 321
Effective search space:    92769
Effective search space used:    92769
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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