GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cscB in Escherichia coli BW25113

Align Oligosaccharide:H+ symporter family protein (characterized, see rationale)
to candidate 14481 b0343 galactoside permease (NCBI)

Query= uniprot:Q4KBP0
         (429 letters)



>FitnessBrowser__Keio:14481
          Length = 417

 Score =  294 bits (752), Expect = 4e-84
 Identities = 158/407 (38%), Positives = 235/407 (57%), Gaps = 5/407 (1%)

Query: 1   MQFAAKREYWLISGLLFFFFFSWSSSYSLFSIWLHRVIGLNGTETGFIFAANAIAALLVQ 60
           M +     +W+     FF+FF   + +  F IWLH +  ++ ++TG IFAA ++ +LL Q
Sbjct: 1   MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQ 60

Query: 61  PFYGALQDRLGLSKKLLVWIGILLCAAAPFAIYVYAGLLAQNVMLGALVGAAFLALAMLA 120
           P +G L D+LGL K LL  I  +L   APF I+++  LL  N+++G++VG  +L     A
Sbjct: 61  PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA 120

Query: 121 GVGVIESYTERLSRHAGFEFGTTRMWGSLGWASATGVVGVVFNIDPDIAFYMSSLAGIVF 180
           G   +E++ E++SR + FEFG  RM+G +GWA    +VG++F I+    F++ S   ++ 
Sbjct: 121 GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALIL 180

Query: 181 LLILF--RLDLDRLAQPAVQAGAVVHPVRLNDLWKLLALPRFWAFSLYLTGVCGIYMIYE 238
            ++LF  + D    A  A   GA      L    +L   P+ W  SLY+ GV   Y +++
Sbjct: 181 AVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFD 240

Query: 239 QQFPVYFSSFFPTPEEGTRAYGYLNSSQVLVEAVLMLLAPWVVSRTGAKYGLILAGSIMF 298
           QQF  +F+SFF T E+GTR +GY+ +   L+ A +M  AP +++R G K  L+LAG+IM 
Sbjct: 241 QQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMS 300

Query: 299 VRILGSGLVTQAWAIAACKMLHALEVPILLVSIFKYISLNFDSRLSASIYLVGFQFAQQL 358
           VRI+GS   T A  +   K LH  EVP LLV  FKYI+  F+ R SA+IYLV F F +QL
Sbjct: 301 VRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL 360

Query: 359 TAMLLSPLVGYGYDHFGFSSVYVLMAGLV--GACLLLSWTLLRKDPV 403
             + +S L G  Y+  GF   Y L+ GLV  G  L+  +TL    P+
Sbjct: 361 AMIFMSVLAGNMYESIGFQGAY-LVLGLVALGFTLISVFTLSGPGPL 406


Lambda     K      H
   0.329    0.142    0.441 

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: 461
Number of extensions: 21
Number of successful extensions: 2
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: 429
Length of database: 417
Length adjustment: 32
Effective length of query: 397
Effective length of database: 385
Effective search space:   152845
Effective search space used:   152845
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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