GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Shewanella loihica PV-4

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__PV4:5207560
          Length = 369

 Score =  147 bits (372), Expect = 3e-40
 Identities = 102/268 (38%), Positives = 147/268 (54%), Gaps = 17/268 (6%)

Query: 29  GELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVND------VPPAQRGIAMVFQ 82
           GE++  VGPSG GKSTL+RMIAGL K   G +    +V         + P QR +  V Q
Sbjct: 29  GEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRYLTPQQRHLGYVPQ 88

Query: 83  SYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQRQRV 142
            + L+P+MT   N+  AL    K  AE  A  +   E++ L    DRLP  LSGGQRQRV
Sbjct: 89  HFGLFPNMTALANVVAALDHIPK--AERVARAKDWLERVNLHGLPDRLPANLSGGQRQRV 146

Query: 143 AIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQVEAMTLA 202
           A+ R++ R+P+V L DEP S +D   R    LE+A+LKE +    ++ VTHD  EA+ LA
Sbjct: 147 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQL-AIPVIMVTHDLNEALLLA 205

Query: 203 TRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQTTVE-MTDG 261
            R+++++ G + Q GSP E+  +P NE VA+ +G    NL    ++   A+  +  +  G
Sbjct: 206 DRMILISQGTLLQQGSPREVLSRPRNEAVAKQMG--LRNLFDAHVVAQEAERQITWLRFG 263

Query: 262 GRAVSDYPSDDSLMGAAV-----NVGVR 284
              ++    +   +GA V     N GVR
Sbjct: 264 EHLIAGNYCEQLAIGAKVRWVIPNQGVR 291


Lambda     K      H
   0.316    0.135    0.379 

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: 274
Number of extensions: 10
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: 373
Length of database: 369
Length adjustment: 30
Effective length of query: 343
Effective length of database: 339
Effective search space:   116277
Effective search space used:   116277
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 (21.6 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