GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcB in Herbaspirillum seropedicae SmR1

Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate HSERO_RS03635 HSERO_RS03635 sugar ABC transporter periplasmic protein

Query= uniprot:A0A0C4Y591
         (325 letters)



>FitnessBrowser__HerbieS:HSERO_RS03635
          Length = 316

 Score =  337 bits (865), Expect = 2e-97
 Identities = 180/311 (57%), Positives = 225/311 (72%), Gaps = 9/311 (2%)

Query: 13  ALSLLCTGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKINPD 72
           A S L   AAAQ A        AA +PLK VGVT+G L NP+FVA+A GAE+ A KINPD
Sbjct: 9   ACSTLLLAAAAQPA-------MAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPD 61

Query: 73  AKVTVLSADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVA 132
           AKVTV+S+ YDLN Q   I++FI +KVDLI++NAAD++ + PAV+KA+KAGIVVVAVDVA
Sbjct: 62  AKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVA 121

Query: 133 AAGADATVQTDNTRAGELACAFLAGRLGGRGNLIIQNGPPVSAVLDRVKGCKMVLGKHPG 192
           AAGAD TV +DNT AG  +C FLA +L G+GN++I NGPPVSAV+DRV GCK    K PG
Sbjct: 122 AAGADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPG 181

Query: 193 IHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNRGGI-LI 251
           I +LSD+Q+  GSR+GG+  M   L   PKIDAVF INDP A+GA+LA RQ  R  I  I
Sbjct: 182 IKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWI 241

Query: 252 ASVDGAPDIEAALK-ANTLVQASASQDPWAIARTAVEIGVGLMHGQAPANRTVLLPPTLV 310
           + VDGAPD E ALK + +L  AS +QDP+ +A  +V IG  +M+G+AP  +  LLP  L+
Sbjct: 242 SGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKLI 301

Query: 311 TRANVNEYKGW 321
           TR NV +Y+GW
Sbjct: 302 TRDNVADYQGW 312


Lambda     K      H
   0.318    0.132    0.377 

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: 246
Number of extensions: 7
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: 325
Length of database: 316
Length adjustment: 28
Effective length of query: 297
Effective length of database: 288
Effective search space:    85536
Effective search space used:    85536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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