GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc02031 SMc02031 permease
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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