GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Desulfoscipio geothermicus DSM 3669

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_092481662.1 BM299_RS00225 amino acid ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_900115975.1:WP_092481662.1
          Length = 240

 Score =  280 bits (716), Expect = 2e-80
 Identities = 144/242 (59%), Positives = 177/242 (73%), Gaps = 3/242 (1%)

Query: 8   LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEV 67
           +I  + L K+FG L+VL+G+  EI  ++V+ +IGPSG GKSTFLRCLN LE I+ G++ V
Sbjct: 1   MIKVENLHKSFGELEVLKGIDCEIAEREVVCVIGPSGSGKSTFLRCLNLLEGITSGKVIV 60

Query: 68  AGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRA 127
            G DL+  K D   + ++R  VGMVFQ FNLFPH+T LQN+ LAP K L +P  +    A
Sbjct: 61  NGHDLTDPKTD---INKVRTEVGMVFQQFNLFPHMTALQNVTLAPVKGLGLPRDQVNQTA 117

Query: 128 LTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLN 187
           L  L+KVGL  KA  YP  LSGGQ QRVAIAR L M P I+LFDEPTSALDPELVGEVL 
Sbjct: 118 LKLLEKVGLSDKAHVYPQNLSGGQMQRVAIARALAMNPRIMLFDEPTSALDPELVGEVLT 177

Query: 188 VMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLS 247
           VMK+LA EGMTM VVTHEM FAREV++RV F + G+I EE  P E+F NP+++R RAFL+
Sbjct: 178 VMKELAREGMTMVVVTHEMGFAREVADRVIFMDHGVIVEENTPQEIFTNPQNERTRAFLN 237

Query: 248 RI 249
            I
Sbjct: 238 MI 239


Lambda     K      H
   0.321    0.139    0.397 

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: 207
Number of extensions: 6
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: 252
Length of database: 240
Length adjustment: 24
Effective length of query: 228
Effective length of database: 216
Effective search space:    49248
Effective search space used:    49248
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: 46 (22.3 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