GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisP in Shewanella sp. ANA-3

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 7025581 Shewana3_2732 phosphate ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9HU32
         (257 letters)



>lcl|FitnessBrowser__ANA3:7025581 Shewana3_2732 phosphate ABC
           transporter, ATPase subunit (RefSeq)
          Length = 272

 Score =  140 bits (353), Expect = 3e-38
 Identities = 98/263 (37%), Positives = 142/263 (53%), Gaps = 22/263 (8%)

Query: 1   MAEATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCIN----LL 56
           +++   ALEIRNL  RYGD + L  +S+      V + +G SG GKST LRCIN    L+
Sbjct: 19  LSQNDTALEIRNLDLRYGDKQALFNVSMKIPKKQVTAFIGPSGCGKSTLLRCINRMNDLV 78

Query: 57  ENPH-QGQILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNV 115
           +N H  G+IL+ G+ +  KK      VAA       LR  +G VFQ  N +P  SI +NV
Sbjct: 79  DNCHIDGEILLHGQNIYDKKID----VAA-------LRRNVGMVFQRPNPFPK-SIYENV 126

Query: 116 IEAPRRVLGKSKAEAIEIAEGLLAKVGI----ADKRHSYPAQLSGGQQQRAAIARTLAMQ 171
           +   R     ++ E  E AE  L    I     D+ H     LSGGQQQR  IAR +A++
Sbjct: 127 VYGLRLQGINNRRELDEAAERSLRGAAIWDEVKDRLHDNAFGLSGGQQQRLVIARAIAIE 186

Query: 172 PKVILFDEPTSALDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLV 231
           P+V+L DEPTSALDP     +  +I  L  +  T+++VTH M  A +VS +  F++ G +
Sbjct: 187 PEVLLLDEPTSALDPISTLTIEELITELKTK-YTVVIVTHNMQQAARVSDQTAFMYMGEL 245

Query: 232 EEQGTPQQVFENPQSARCKQFMS 254
            E      +F  P+  + + +++
Sbjct: 246 VEYADTNTIFTTPKKRKTEDYIT 268


Lambda     K      H
   0.317    0.133    0.367 

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: 135
Number of extensions: 5
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: 257
Length of database: 272
Length adjustment: 25
Effective length of query: 232
Effective length of database: 247
Effective search space:    57304
Effective search space used:    57304
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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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