GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Escherichia coli BW25113

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__Keio:18063
          Length = 371

 Score =  299 bits (765), Expect = 9e-86
 Identities = 168/360 (46%), Positives = 221/360 (61%), Gaps = 28/360 (7%)

Query: 1   MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60
           MA +Q  N+ K++G   V K I+LDI  GEF+V VGPSGCGKSTLLR +AGLE+  SG +
Sbjct: 1   MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60

Query: 61  SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120
            I  K++ND  P  R + MVFQSYALYPH++VAENM FGLKL       I +RVN+++E+
Sbjct: 61  FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120

Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180
           LQ+ HLLDRKPK LSGGQRQRVA+GR L  +  V L DEPLSNLDA LR QMR+EI RLH
Sbjct: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180

Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240
                TMIYVTHDQ+EA TL D+I VL  G + Q+G P E+YH P + F+A FIGSP+MN
Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240

Query: 241 FLE--------GAVLEKIPWPEARK-------------ADQILGIRPDAFALNQGPLGTQ 279
           FL           V  ++P P  ++             A+  LGIRP+       P    
Sbjct: 241 FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLL----PSDIA 296

Query: 280 EVALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQ--TLPLKIDLTKAHLF 337
           +V L + ++ + E LG +  +H  +      ++    D   +++  T  + +   + HLF
Sbjct: 297 DVIL-EGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLF 355


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: 347
Number of extensions: 15
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: 371
Length adjustment: 29
Effective length of query: 318
Effective length of database: 342
Effective search space:   108756
Effective search space used:   108756
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:

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