GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03635 in Paraburkholderia bryophila 376MFSha3.1

Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate H281DRAFT_04150 H281DRAFT_04150 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= uniprot:D8IZC6
         (316 letters)



>FitnessBrowser__Burk376:H281DRAFT_04150
          Length = 317

 Score =  173 bits (438), Expect = 6e-48
 Identities = 110/296 (37%), Positives = 169/296 (57%), Gaps = 9/296 (3%)

Query: 15  LAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDLN 74
           L+  A PA  A  PLK +G+T  +L NP+FV + K     A   +  A V V  + +D++
Sbjct: 28  LSMIAVPAAQA-APLK-IGMTFQELNNPYFVTMQKALNDAA--ASTGATVIVTDAHHDVS 83

Query: 75  TQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAG-ADVTVMSDN 133
            QV  +E+ +  K+D++++N  DS G+  AV  A+KAG+VVVAVD  A G  D  V S N
Sbjct: 84  KQVSDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVVAVDANANGPVDSFVGSKN 143

Query: 134 TMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKSPGIKILSDNQNAGG 193
             AG  +C++L++ + G G V I++G PV  +++RV GCKA   KSPG+K++ D QN   
Sbjct: 144 FDAGQMACEYLSKSIGGSGEVAILDGIPVVPILERVRGCKAALAKSPGVKLV-DTQNGKQ 202

Query: 194 SRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIKWISGVDGAPDAERA 253
            R   ++   N++ A P +  VF++ND  ++GA  AI ++   DIK ++ VDGAP+A  A
Sbjct: 203 ERATALSVTENMIQAHPNLKGVFSVNDGGSMGALSAI-ESSGKDIK-LTSVDGAPEAIAA 260

Query: 254 LKDSKSLFAASPAQDPYGMAAESVAIGYAVMNGRAPQQKVKLLPVKLITRDNVADY 309
           ++   S F  + AQ P      ++ I YA   G A   K   + VK+I + N   +
Sbjct: 261 IQKPNSKFVETSAQFPADQVRIALGIAYAKKWG-ANVPKAIPVDVKMIDKSNAKGF 315


Lambda     K      H
   0.314    0.129    0.360 

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: 208
Number of extensions: 13
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: 316
Length of database: 317
Length adjustment: 27
Effective length of query: 289
Effective length of database: 290
Effective search space:    83810
Effective search space used:    83810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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