GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Desulfacinum infernum DSM 9756

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:Q6MNM2
         (347 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  296 bits (759), Expect = 4e-85
 Identities = 162/361 (44%), Positives = 219/361 (60%), Gaps = 20/361 (5%)

Query: 1   MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60
           MA+I+   + K F    V++   L +A  EF+VLVGPSGCGKST LR +AGLE   SG I
Sbjct: 1   MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60

Query: 61  SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120
           SI G+ +N + P++RDIAMVFQSYALYPHM V +NM FGL  + +   EI +RV + +E+
Sbjct: 61  SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120

Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180
           L I  LL R+P +LSGGQRQRVA+GRA+ R     LFDEPLSNLDA LR QMR E+ +LH
Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180

Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240
              +ST++YVTHDQ+EA TL DRI V+KDG I Q+G P E+Y RP N F+A FIGSP MN
Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240

Query: 241 FLEGAVLE--------------KIPWPEAR------KADQILGIRPDAFALNQGPLGTQE 280
           FL+  ++E              K+P   A           I GIRP+      G    + 
Sbjct: 241 FLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALPEG 300

Query: 281 VALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKK 340
           V     ++D+ E +G + ++  T+  +     +       +   + L +++ K HLFD +
Sbjct: 301 VEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHLFDPE 360

Query: 341 T 341
           +
Sbjct: 361 S 361


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: 331
Number of extensions: 10
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: 347
Length of database: 368
Length adjustment: 29
Effective length of query: 318
Effective length of database: 339
Effective search space:   107802
Effective search space used:   107802
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 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