GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Malonomonas rubra DSM 5091

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= uniprot:A0A1N7U8S3
         (276 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  129 bits (325), Expect = 8e-35
 Identities = 93/268 (34%), Positives = 146/268 (54%), Gaps = 22/268 (8%)

Query: 11  YPVDEPVAQPVTAAIK--LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTM 68
           Y +  P  +   A +K  L  E I ++      ++  S    +G++  ++G SGSGKSTM
Sbjct: 13  YKIFGPQPKKAMALLKQGLDKEAIFEKTETTVGVQDASFEIFKGEIFVIMGLSGSGKSTM 72

Query: 69  LRCINFLEQPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLR-TRLAMVFQHFNLWSHM 127
           +R +N L +P +G + +DG  I          A + DQL  +R  +L+MVFQ F L  HM
Sbjct: 73  VRMLNRLIEPTSGQVLIDGEDIV---------AMNDDQLVKVRRAKLSMVFQSFALMPHM 123

Query: 128 TVLENITMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARAL 187
           TVL+N       +  V     E+RA   L++VGL +  A+  P  LSGG QQRV +AR L
Sbjct: 124 TVLQNAAFG-LEMDGVDKQTREQRALQALEQVGLEAW-AESMPDELSGGMQQRVGLARGL 181

Query: 188 AMEPEIILFDEPTSALDP----ELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVL 243
           A++P+I+L DE  SALDP    E+  E+LK+    A+  RT++ ++H++  A ++  ++ 
Sbjct: 182 AVDPDILLMDEAFSALDPLIRTEMQDELLKL---QAKAKRTIVFISHDLDEAMRIGDRIA 238

Query: 244 FLHQGRVEEHG-DARILDQPNSERLQQF 270
            +  GRV + G    IL  P  + ++ F
Sbjct: 239 IMEGGRVVQVGTPEEILQNPADDYVRAF 266


Lambda     K      H
   0.319    0.133    0.372 

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: 255
Number of extensions: 14
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: 276
Length of database: 415
Length adjustment: 28
Effective length of query: 248
Effective length of database: 387
Effective search space:    95976
Effective search space used:    95976
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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