GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Halomonas xinjiangensis TRM 0175

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  300 bits (769), Expect = 3e-86
 Identities = 175/364 (48%), Positives = 229/364 (62%), Gaps = 20/364 (5%)

Query: 1   MAPVTLKKLVKRY-GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59
           MA + L  L K Y G +E V GIDLE+ D EF+ LVGPSGCGKST LRM+AGLE ++ G 
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119
           ++I  R VNDL P  R+I+MVFQ+YALYPHMTV  N+ + LK  G   EEI+ RV +AAA
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179
           +L++   LER+P +LSGGQRQRVAMGRA+VR+P  FLFDEPLSNLDAKLR Q+R EIK+L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239
             R++ T +YVTHDQ+EA+TL DR+V++  G IEQVGTP +V+ +PA+ FVA FIGSP M
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 240 NMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAV 299
           NM        +   A+G    L                G+RPDD+      + A D D +
Sbjct: 241 NMLPVAYL--RERGANGLLDHL---------AADTDVIGIRPDDL-----RIEAPDEDHL 284

Query: 300 HEIELPVTITEPLGNETLVFTQFNGRD--WVSRMLNPRPLRPGEAVPMSFDLARAHLFDG 357
             +   V + E  G E+ ++    G D   V R     P+  GE +      +  H F+ 
Sbjct: 285 -VVTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFNQ 343

Query: 358 ETGR 361
            +G+
Sbjct: 344 ASGK 347


Lambda     K      H
   0.320    0.137    0.397 

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: 384
Number of extensions: 18
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: 365
Length of database: 354
Length adjustment: 29
Effective length of query: 336
Effective length of database: 325
Effective search space:   109200
Effective search space used:   109200
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 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