GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Sinorhizobium meliloti 1021

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate SM_b20661 SM_b20661 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__Smeli:SM_b20661
          Length = 355

 Score =  318 bits (814), Expect = 2e-91
 Identities = 174/358 (48%), Positives = 227/358 (63%), Gaps = 24/358 (6%)

Query: 1   MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60
           MA + F +++KSFG+  V+KG++++I  GEF++LVGPSGCGKSTLLR LAGLE+  +G I
Sbjct: 1   MAGVDFVDVRKSFGAFPVIKGVNIEIEDGEFVILVGPSGCGKSTLLRMLAGLENITAGEI 60

Query: 61  SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120
            I  + +N + P++RDIAMVFQ+YALYPHMTVA+NM F L L     +EI KRV   +E+
Sbjct: 61  RIGNQVVNRLPPKDRDIAMVFQNYALYPHMTVADNMAFSLMLAARPKSEIDKRVGVAAEI 120

Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180
           L +  LLDR P++LSGGQRQRVA+GRA+ R   V LFDEPLSNLDA LR  MR EIK LH
Sbjct: 121 LGLSKLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKELH 180

Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240
              K+T +YVTHDQ+EA T+ D+I V+ DG++EQIG P E+Y  P N F+A FIGSP MN
Sbjct: 181 QRLKTTTVYVTHDQIEAMTMADKIVVMHDGIVEQIGAPLELYDNPANLFVAGFIGSPAMN 240

Query: 241 FLEGAVLEKIP----------WPEARKA------DQILGIRPDAFALNQGPLGTQEVALG 284
            L+G +    P           P AR A      D + G+RP+  AL+   L        
Sbjct: 241 MLKGRLDPADPSVFLTADGTALPVARPAAAAQGRDLVYGLRPEYMALDPNGLPA------ 294

Query: 285 DFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342
             +I + E  G +  L   L G++V  +     N    +T+ L ID    HLFD  TG
Sbjct: 295 --EIAVIEPTGYETQLIARLGGHDVTCVFRERVNAKPGETIHLAIDAAHVHLFDAGTG 350


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: 343
Number of extensions: 13
Number of successful extensions: 2
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: 355
Length adjustment: 29
Effective length of query: 318
Effective length of database: 326
Effective search space:   103668
Effective search space used:   103668
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