GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Sinorhizobium meliloti 1021

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate SMc02772 SMc02772 sugar ABC transporter permease

Query= SwissProt::P37772
         (331 letters)



>FitnessBrowser__Smeli:SMc02772
          Length = 324

 Score =  153 bits (386), Expect = 6e-42
 Identities = 106/302 (35%), Positives = 158/302 (52%), Gaps = 13/302 (4%)

Query: 10  ITIGVFVLGYLYCLTQFPGFASTRV-----ICNILTDNAFLGIIAVGMTFVILSGGIDLS 64
           I  G+ ++G L  L    G A+        I N+L   A   I+AVG TFVI++ GIDLS
Sbjct: 19  ILFGLTLVGLLVVLWLLLGLATNAFWTPNNISNLLRQGAMTAILAVGQTFVIITAGIDLS 78

Query: 65  VGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGM 124
           VG+V+ FT V +A ++   G+   LA    L +G   GAF    I  + +P FIITLA +
Sbjct: 79  VGAVVGFTSVIVAWLLAA-GVPLWLAIIATLAIGVLIGAFHAFGIVRMGLPPFIITLATL 137

Query: 125 FFLRGVSYLVSEES-IPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRT 183
             LRG+  L++  S I I +  + T S   +     G  S   ++++  +   +FL H +
Sbjct: 138 TSLRGIGLLITNGSTISITNDAFTTFSRADFL----GIPSLFWMVIVVAIPAYVFL-HLS 192

Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGV 243
           RFG  ++A+G N+ +A L G++   T    Y+LS+  A   G++ +     G A    G 
Sbjct: 193 RFGRYLFAVGSNSEAARLSGVNVNRTIYLAYILSSTCAAFVGLLLASRIGIGNATQAEGW 252

Query: 244 ELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFI 303
           EL AIAS VIGGT L G VG+V G L G  I   I    N    ++S+W +I  G+L+ +
Sbjct: 253 ELQAIASSVIGGTSLFGAVGSVHGPLLGAFILATINNGANL-LNVNSFWQRIITGLLIIV 311

Query: 304 FI 305
            +
Sbjct: 312 IV 313


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: 337
Number of extensions: 22
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: 324
Length adjustment: 28
Effective length of query: 303
Effective length of database: 296
Effective search space:    89688
Effective search space used:    89688
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: 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