GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Escherichia coli BW25113

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= SwissProt::P37772
         (331 letters)



>FitnessBrowser__Keio:16645
          Length = 332

 Score =  166 bits (420), Expect = 8e-46
 Identities = 105/306 (34%), Positives = 172/306 (56%), Gaps = 10/306 (3%)

Query: 2   IKRNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGI 61
           + R++  +  + V  + YL      PGF S     N+L D A +GI A  MT +I+SG I
Sbjct: 20  VSRHINEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEI 79

Query: 62  DLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITL 121
           D+SVG ++AF  V LA ++  F +   +A  LVL++G   G   G+L     +P+F+ TL
Sbjct: 80  DVSVGPMVAFVSVCLAFLL-QFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATL 138

Query: 122 AGMFFLRGVS-YLVSEESIPIN-HPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFL 179
                LRG+  ++ +   +PI+ + + D L      +P         L+M+ +  + +F+
Sbjct: 139 GLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVP------VSALIMIVLFALFVFI 192

Query: 180 AHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALA 239
           + +T FG  V+A+GGNAT+A L GI+ R   I I+ LS  LA + GI+ +    +G A A
Sbjct: 193 SRKTAFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGA 252

Query: 240 GVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGI 299
             G+E D IA+VV+GGT LSGG G++ GTL GV +  LI   +   G ++S++ ++  G+
Sbjct: 253 ANGLEFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLG-INSFFQQVVRGV 311

Query: 300 LLFIFI 305
           ++ + +
Sbjct: 312 IIVVAV 317


Lambda     K      H
   0.329    0.145    0.428 

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: 310
Number of extensions: 18
Number of successful extensions: 3
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: 331
Length of database: 332
Length adjustment: 28
Effective length of query: 303
Effective length of database: 304
Effective search space:    92112
Effective search space used:    92112
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: 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