GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK_Bb in Marinobacter adhaerens HP15

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= uniprot:Q6MNM2
         (347 letters)



>lcl|FitnessBrowser__Marino:GFF3011 HP15_2955 ATP-binding component
           of ABC transporter
          Length = 372

 Score =  324 bits (830), Expect = 3e-93
 Identities = 178/366 (48%), Positives = 243/366 (66%), Gaps = 26/366 (7%)

Query: 1   MAKIQFSNIKKSFGSA--DVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58
           M++++  +I+K++     + LKGID+DIA GEFL+LVGPSGCGKSTL+ T+AGLE+   G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 59  TISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEIS 118
           +I +DGK I+ +EP++RDIAMVFQSYALYP M+V EN+ FGLK++ L   EI + V  ++
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 119 ELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKR 178
           +LLQI  L+++KP  LSGGQ+QRVA+GRAL+R+  + LFDEPLSNLDA LR +MR EIK+
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 179 LHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPE 238
           LH   K+T++YVTHDQ+EA TL DRIAVLKDG ++Q+GTP E+Y RP+N F+A F+GSP 
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 239 MNFLEGAVLE-----------------KIPWPEARKADQ-----ILGIRPDAFALNQGPL 276
           M+F+   V +                 K+P PE   AD+     ILGIRP+     Q   
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEF-LADRVGKKVILGIRPEHITQPQDQK 299

Query: 277 GTQE-VALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAH 335
             Q  VA G+F I+++E  G   +    L   NV   +D     +  +T  L  D+ K  
Sbjct: 300 NDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKVV 359

Query: 336 LFDKKT 341
            FD +T
Sbjct: 360 FFDPET 365


Lambda     K      H
   0.318    0.136    0.383 

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: 379
Number of extensions: 16
Number of successful extensions: 1
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: 347
Length of database: 372
Length adjustment: 29
Effective length of query: 318
Effective length of database: 343
Effective search space:   109074
Effective search space used:   109074
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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