GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Shewanella loihica PV-4

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  162 bits (410), Expect = 1e-44
 Identities = 89/210 (42%), Positives = 132/210 (62%), Gaps = 8/210 (3%)

Query: 4   VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63
           + I+ VS++F+  +     A+  V   +   +   +LG SG GKSTLLR++AG +  T G
Sbjct: 21  LKIERVSKLFDDVR-----AVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEG 75

Query: 64  RVLLDGAPV-EGPGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFI 120
           R+ LDG  + + P  ER   M+FQSY LFP +T+ QNI FGL++  MP+A+ ++R    +
Sbjct: 76  RIYLDGQDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEML 135

Query: 121 AKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLG 180
             V +  + +  P QLSGG +QR A+AR+LA  PK+LL+DEP GALD + R  MQ  ++ 
Sbjct: 136 KLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVD 195

Query: 181 IWEAERKTVLFVTHDIDEAIFMANRVAVFS 210
           I EA   T + VTHD +EA+ MA R+A+ +
Sbjct: 196 ILEAVGVTCVMVTHDQEEAMTMAERIAIMN 225


Lambda     K      H
   0.322    0.136    0.394 

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: 191
Number of extensions: 7
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: 259
Length of database: 378
Length adjustment: 27
Effective length of query: 232
Effective length of database: 351
Effective search space:    81432
Effective search space used:    81432
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 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