GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Halomonas xinjiangensis TRM 0175

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= CharProtDB::CH_024626
         (378 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  247 bits (630), Expect = 4e-70
 Identities = 132/292 (45%), Positives = 192/292 (65%), Gaps = 13/292 (4%)

Query: 18  VQLAGIRKCFDGK-EVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIML 76
           +QL G++K + G  E +  +DL I +GEF+ L+GPSGCGK+T+LR++AGLET+  G + +
Sbjct: 4   IQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGTLKI 63

Query: 77  DNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQ 136
           D+  +  +    R +  VFQ+YAL+PHMTVF N+A+GL+ +     EI  RV +A  M++
Sbjct: 64  DDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAAMLE 123

Query: 137 LETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRK 196
           +E F +RKP +LSGGQ+QRVA+ RA+V +P   L DE LS LD KLR QM+ E+K LQR+
Sbjct: 124 IEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQLQRR 183

Query: 197 LGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNA 256
           L  T ++VTHDQ EALT+ DR+VV+  G IEQ GTP E+YE+P ++FVA FIG   M N 
Sbjct: 184 LKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM-NM 242

Query: 257 TVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDN 308
             +  L E+     ++    +  V           + +RP+DLR+E  ++D+
Sbjct: 243 LPVAYLRERGANGLLDHLAADTDV-----------IGIRPDDLRIEAPDEDH 283


Lambda     K      H
   0.319    0.136    0.385 

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: 344
Number of extensions: 15
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: 378
Length of database: 354
Length adjustment: 30
Effective length of query: 348
Effective length of database: 324
Effective search space:   112752
Effective search space used:   112752
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 (21.7 bits)
S2: 49 (23.5 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