GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Desulfacinum infernum DSM 9756

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1302
         (334 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  295 bits (755), Expect = 1e-84
 Identities = 165/342 (48%), Positives = 218/342 (63%), Gaps = 24/342 (7%)

Query: 3   QIKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRI 62
           QI++  V K++G V+ +  +  ++E+G+  V +GPSGCGK+TLLRLIAGLE +TSGTI I
Sbjct: 2   QIEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHI 61

Query: 63  DGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALN 122
            G D T++PP KR ++MVFQSYAL+PH++VR+NI F +K+  +PADE +RR+      L 
Sbjct: 62  AGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLG 121

Query: 123 LTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKR 182
           L+  LD +PG+LSGG +QRVA+GRAI+ E    L DEPLSNLDA LR  MR EI  L +R
Sbjct: 122 LSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRR 181

Query: 183 LATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLL 242
           L  TMIYVTHDQVEAMTMAD+IV+++ G I Q  SP   Y  P N FVA FIG+P MN++
Sbjct: 182 LGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIV 241

Query: 243 TGPQAAQHNAATI------------------GIRPEHLSISETEGMWAGTIGVSEHLGSD 284
             P       A +                  GIRPE+L ++E+ G  A   G  E+LGSD
Sbjct: 242 --PLCPTQGGAALEPGGRLLFPGMDPDRYLFGIRPENLRLAES-GQPAMVTG-REYLGSD 297

Query: 285 TFFHVQCDAFDDPLTVRASGELDLGYGERVFLTPDMTHLHRF 326
           TF  V C+     + VR  G  ++  G  V LT D   ++ F
Sbjct: 298 TF--VSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLF 337


Lambda     K      H
   0.320    0.138    0.400 

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: 358
Number of extensions: 14
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: 334
Length of database: 365
Length adjustment: 29
Effective length of query: 305
Effective length of database: 336
Effective search space:   102480
Effective search space used:   102480
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 (21.8 bits)
S2: 49 (23.5 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