GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Dinoroseobacter shibae DFL-12

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 3606953 Dshi_0381 ABC transporter related (RefSeq)

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__Dino:3606953
          Length = 274

 Score =  207 bits (528), Expect = 1e-58
 Identities = 111/246 (45%), Positives = 161/246 (65%), Gaps = 8/246 (3%)

Query: 4   KSNKVLLQVKGLKVAYGGIQAV-KGVDFEVREGELVSLIGSNGAGKTTTMKAITGTL--- 59
           ++ + LL+V  ++V Y  +  V KGV   V +G + +L+G NGAGKTTT+K+I+  L   
Sbjct: 6   RTEETLLEVNNIEVIYNHVILVLKGVSLTVPKGGITALLGGNGAGKTTTLKSISNLLHSE 65

Query: 60  --SMNDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAG 117
              +  G I Y G  ++     D+VK G++ V EGR  F  +T+ ENL  GAY R+D  G
Sbjct: 66  RGEVTKGTISYRGDRVQDLSPSDMVKRGVIQVMEGRHCFEHLTVEENLLTGAYTRRDGRG 125

Query: 118 ILAD-IEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPI 176
            +AD +E ++T FPRL+ER+   AG  SGGEQQM A+GRALMS+P+ +LLDEPSMGL+P 
Sbjct: 126 AIADDLELVYTYFPRLKERRKSQAGYTSGGEQQMCAIGRALMSRPETILLDEPSMGLAPQ 185

Query: 177 MVDKIFEVVRDVYAL-GVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKV 235
           +V++IF +V+++    GV+ +L EQN + AL  A  GY++ESG + M GP  +L  +P V
Sbjct: 186 LVEEIFTIVKNLNEREGVSFLLAEQNTNVALRFAHHGYILESGRVVMEGPAAELRENPDV 245

Query: 236 RAAYLG 241
           +  YLG
Sbjct: 246 KEFYLG 251


Lambda     K      H
   0.317    0.136    0.373 

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: 200
Number of extensions: 9
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: 242
Length of database: 274
Length adjustment: 24
Effective length of query: 218
Effective length of database: 250
Effective search space:    54500
Effective search space used:    54500
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: 47 (22.7 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