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 SM_b20352 SM_b20352 sugar ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>lcl|FitnessBrowser__Smeli:SM_b20352 SM_b20352 sugar ABC transporter
           permease
          Length = 354

 Score =  246 bits (628), Expect = 6e-70
 Identities = 134/323 (41%), Positives = 204/323 (63%), Gaps = 19/323 (5%)

Query: 9   TFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAID 68
           T  +L   +AL ++  F +I  P FL+  NL  + + +A+   LA+G TFVII+GG  ID
Sbjct: 21  TLMKLRTFIALFAVVAFFSIFAPNFLSTANLILMSKHVALNAFLAMGMTFVIITGG--ID 78

Query: 69  LSPGSMVALTGVMVAWLMTHGVP------VWISVILILLFSIGAG----AWHGLFVTKLR 118
           LS GS+V L G++   L+ +G+       V+ +V+ + L ++  G    A +GL +TKL 
Sbjct: 79  LSVGSIVGLCGMVAGGLILNGIDLQFGYTVYFNVVEVCLITLAVGIVIGAVNGLLITKLN 138

Query: 119 VPAFIITLGTLTIARGMAAVITKGWP---IIGLP----SSFLKIGQGEFLKIPIPVWILL 171
           V  FI TLGTL +ARG A + + G     ++G P    + F  +G G  L +P+ +W+L+
Sbjct: 139 VAPFIATLGTLYVARGFALLSSGGQTFPNLVGKPELATTGFAFLGSGRLLGLPVSIWVLI 198

Query: 172 AVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAA 231
            VAL A +  R T  G+H+ A GGNE AAR SG+ VDRV+M  +M SGF A +VG++I++
Sbjct: 199 VVALAAAYVARYTPIGRHIFAVGGNERAARMSGIRVDRVKMFVYMFSGFCAAIVGLVISS 258

Query: 232 RLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTY 291
            L    P  G+ +EL AIA+ V+GGTS++GG G++ G I+GA +I +L + LV++ +S++
Sbjct: 259 ELMASHPATGNSFELNAIAAAVLGGTSMSGGRGTIGGTIIGAFVIGILSDGLVMMGISSF 318

Query: 292 WHNVVIGIVIVVAVTLDILRRRL 314
           W  V+ GIVI+VAV +D  +RRL
Sbjct: 319 WQMVIKGIVIIVAVVVDQAQRRL 341


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: 346
Number of extensions: 24
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: 354
Length adjustment: 28
Effective length of query: 289
Effective length of database: 326
Effective search space:    94214
Effective search space used:    94214
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