GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Desulfacinum infernum DSM 9756

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= SwissProt::Q9YGA6
         (372 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  298 bits (764), Expect = 1e-85
 Identities = 173/371 (46%), Positives = 230/371 (61%), Gaps = 31/371 (8%)

Query: 4   VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63
           + + DV K +G V AVR +S  V++G+ +++LGPSGCGKTT LR+IAGLE  + G I+I 
Sbjct: 3   IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62

Query: 64  DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123
              V        +PP  R+I+MVFQSYAL+PH+ V +NI F LK+RKVP  EI++R++ V
Sbjct: 63  GTDVTH------LPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRV 116

Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183
            +LLGL+  L+ KP ELSGG +QRVALGRAI+ +  V LMDEPLSNLDAKLR  MR E+ 
Sbjct: 117 VDLLGLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREIC 176

Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243
            LQR+LG+T IYVTHDQVEAMTM DRI +M  G + Q  SP+  Y++PANTFVA FIG+P
Sbjct: 177 SLQRRLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTP 236

Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGRE---VIFGIRPEDLYDAMFA 300
           PMN +    T+ G                E  G L + G +    +FGIRPE+L  A   
Sbjct: 237 PMNIVPLCPTQGGAA-------------LEPGGRLLFPGMDPDRYLFGIRPENLRLAESG 283

Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360
           Q          A+V   E LGS+  V   + G   +   R    +REG  V + +D   +
Sbjct: 284 Q---------PAMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDV 334

Query: 361 HIFDKTTGKAI 371
           ++FD  T + +
Sbjct: 335 NLFDARTQERV 345


Lambda     K      H
   0.323    0.142    0.406 

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: 403
Number of extensions: 16
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: 372
Length of database: 365
Length adjustment: 30
Effective length of query: 342
Effective length of database: 335
Effective search space:   114570
Effective search space used:   114570
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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