Alignments for a candidate for mglA in Desulfacinum hydrothermale DSM 13146

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Desulfacinum hydrothermale DSM 13146

Align glucose transporter, ATPase component (characterized)
to candidate WP_084056628.1 B9A12_RS04270 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>NCBI__GCF_900176285.1:WP_084056628.1
          Length = 702

 Score = 89.4 bits (220), Expect = 2e-22
 Identities = 74/244 (30%), Positives = 117/244 (47%), Gaps = 21/244 (8%)

Query: 14  PLVEMKDISISF----GGIKAVDHVSVDLYPGEVVGLLGHNGAGKST----LIKVLSGAY 65
           P++E++ +SIS+    G I AV  VS  +  GE +GL+G +G GKST    L+  L    
Sbjct: 10  PVLEVEHLSISYKTRRGWIPAVRDVSFQIGAGETLGLVGESGCGKSTVAFSLVNFLGSNG 69

Query: 66  QMDAGEIRVNGDKVEITNPRDA---RSHNIETIYQTLALADNLDAASNLFLGRELVTPFG 122
           ++  G IR  G ++   + R+    R + I  +YQ    A N      L +G +L+    
Sbjct: 70  RIAGGSIRFEGSELVGRSRRELNRLRGNRISMVYQNPMSALN----PTLRIGEQLMEVLT 125

Query: 123 LVDDSAMEAECRKIMNRLNPNFQKFSEPVSA-----LSGGQRQSVAIARAVYFNAKILIM 177
                +      + +  L   +   ++ + A     LSGGQ+Q V IA A+  +  +LIM
Sbjct: 126 CHQTVSKTEAWDRAVAMLRRVYMPDADQIMARYPHQLSGGQQQRVVIAMAMLNHPALLIM 185

Query: 178 DEPTAALGPHETQMVAELIQQLKAQ-GIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVD 236
           DEPT AL       V +L++ LK +    I  I H++  V  + DR  VM  G++V    
Sbjct: 186 DEPTTALDVTVEAAVLDLVEDLKQEFQTSILFITHNLGVVARVSDRLCVMYAGEMVEQGQ 245

Query: 237 IDDV 240
           +D V
Sbjct: 246 VDTV 249



 Score = 85.1 bits (209), Expect = 4e-21
 Identities = 61/245 (24%), Positives = 117/245 (47%), Gaps = 26/245 (10%)

Query: 10  AGATPLVEMKDISISFGG----------------IKAVDHVSVDLYPGEVVGLLGHNGAG 53
           A  +PL++M+++ + +                  ++AVD VS+ +  G  +G++G +G G
Sbjct: 355 AEGSPLLQMREVKVYYEQRKPSLKSLLGLGDKEYVRAVDGVSLRVPRGRTLGIVGESGCG 414

Query: 54  KSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASN--L 111
           KS+L+K + G  ++  G +   G  +  T     R  + E I +   +  N DA  N   
Sbjct: 415 KSSLLKAVIGLERLSGGRLEFLGLDIAKT----VRHRDFEVIREIQMVFQNPDATLNPSY 470

Query: 112 FLGRELVTP---FGLVDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAV 168
            +G+++  P   F  V    + +E  +++  +    + +      LSGG++Q V IARA+
Sbjct: 471 SVGKQIARPIRRFRTVPKGQVRSEVIRLLKAVRLGPEYYDRYPRQLSGGEKQRVGIARAL 530

Query: 169 YFNAKILIMDEPTAALGPHETQMVAELIQQLKAQ-GIGIFLIDHDVNAVMELCDRASVMK 227
                +++ DEP +AL       V  L+ +++ + G  +  I HD++ V    D  +VM 
Sbjct: 531 ASRPDLVLCDEPVSALDVSVQAAVLNLLMEIQEELGTTLLFIAHDLSVVRYFTDDVAVMY 590

Query: 228 NGQLV 232
            GQ++
Sbjct: 591 LGQIM 595


Lambda     K      H
   0.317    0.135    0.373 

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: 364
Number of extensions: 12
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 702
Length adjustment: 32
Effective length of query: 228
Effective length of database: 670
Effective search space:   152760
Effective search space used:   152760
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources