GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Ruegeria conchae TW15

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_120981226.1 G7G_RS0114900 ABC transporter ATP-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>NCBI__GCF_000192475.1:WP_120981226.1
          Length = 366

 Score =  170 bits (431), Expect = 4e-47
 Identities = 94/229 (41%), Positives = 135/229 (58%), Gaps = 8/229 (3%)

Query: 43  GCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMD 102
           G VV   DL+LSIG GE    +G SG GK+T +R       PT G +L+DGE +  LD  
Sbjct: 19  GNVVAAKDLNLSIGKGEFLSFLGPSGCGKTTALRMLAGFEKPTEGQVLLDGEVVNDLDA- 77

Query: 103 ALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGE--SKQVCAERALHWINTVGLKG 160
                    ++MVFQ + L PH SV DN+AYGL+ +     KQ  A +    + TV L G
Sbjct: 78  -----HHRPVNMVFQHYALFPHLSVFDNIAYGLRQQRPHVDKQTIATKVEQALETVRLGG 132

Query: 161 YENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHK 220
           +  +   ++SGG +QRV LARA+  +  ++L+DE  +ALD  +R EMQ +L  LQ+ L  
Sbjct: 133 FGPRRIWEMSGGQQQRVALARAIVNEPKLLLLDEPMAALDRKLRKEMQFELQNLQRQLGI 192

Query: 221 TIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269
           T V +THD +EA+ + +RI +++ G ++QVG+PRE+   P   YV  FV
Sbjct: 193 TFVLVTHDQEEALSMSDRICVMEGGSIVQVGSPRELYDMPRSRYVAGFV 241


Lambda     K      H
   0.321    0.138    0.387 

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: 217
Number of extensions: 7
Number of successful extensions: 3
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: 276
Length of database: 366
Length adjustment: 27
Effective length of query: 249
Effective length of database: 339
Effective search space:    84411
Effective search space used:    84411
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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