GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Pseudomonas simiae WCS417

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__WCS417:GFF2270
          Length = 342

 Score =  229 bits (585), Expect = 6e-65
 Identities = 119/275 (43%), Positives = 176/275 (64%), Gaps = 7/275 (2%)

Query: 1   MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60
           MA +Q + + K +G+ D +   DL +  GEF+ L+GPSGCGK+T L+ +AG      G I
Sbjct: 1   MAFLQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQI 60

Query: 61  SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120
            +DG+ I   +P +R + +VFQSYAL+PHM+V +N+ FGLK++ + AAEI  +V  + EL
Sbjct: 61  LLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLEL 120

Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180
           +++    DR P+ELSGGQRQRVAL RAL  + PV+L DEPLSNLDA+LR +M+ EI+R+ 
Sbjct: 121 VRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180

Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240
                T + VTHDQ EA ++ DR+ V++ G + QI  P ++Y  P+  FI+ F+G  + N
Sbjct: 181 CAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVG--KAN 238

Query: 241 FLEGAVLEKIPWPEAR----KADQILGIRPDAFAL 271
            L G   + +  P+ R      +  L +RP+   L
Sbjct: 239 LLPGD-YDLLGSPQVRHESGDGELTLSLRPEKIQL 272


Lambda     K      H
   0.318    0.136    0.383 

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: 268
Number of extensions: 13
Number of successful extensions: 1
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: 347
Length of database: 342
Length adjustment: 29
Effective length of query: 318
Effective length of database: 313
Effective search space:    99534
Effective search space used:    99534
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: 49 (23.5 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