Alignments for a candidate for mglA in Dethiosulfovibrio salsuginis USBA 82

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Dethiosulfovibrio salsuginis USBA 82

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate WP_085544740.1 B9Y55_RS07445 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_900177735.1:WP_085544740.1
          Length = 497

 Score =  372 bits (956), Expect = e-107
 Identities = 208/488 (42%), Positives = 311/488 (63%), Gaps = 9/488 (1%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEG-E 60
           KP +E+++I KRF GV AL  V +   PGE+H + G+NG+GKSTL+KII+GVY+P++G E
Sbjct: 5   KPFIELRNISKRFGGVTALDDVGLSLSPGEIHCLAGQNGSGKSTLIKIISGVYRPEDGAE 64

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMYR 119
           I  +G  V  + P++AI  GI  ++Q+LS+   LSVAENI +G   EK   F+D  ++  
Sbjct: 65  IFIDGELVALD-PAKAIGIGIQVIYQDLSIFPGLSVAENIGLGQYCEKGRFFVDKGRLVS 123

Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
           +A+  M +  GI +   +K+ + SIA +Q+V I RA+   A+++I+DEPT+SLT+ E + 
Sbjct: 124 DAKTAMNK-IGISLPLRKKVSELSIADRQLVAICRALANDARLVIMDEPTASLTRTEVKA 182

Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           L  VVK LK + +A++F+SHRL+E+ E+ ++V+VLRDG+ +G      L  +K+   M G
Sbjct: 183 LLSVVKELKNRDIAVVFVSHRLDEVIEVAERVTVLRDGKSVGVFEASELDDKKLATYMTG 242

Query: 240 RKLEKFYIKEAHEPGEVVLEVKNLSGE-RFENVSFSLRRGEILGFAGLVGAGRTELMETI 298
            + +   + +      V+L V+ L+ +  +++VSF L RGEILG  GL+G+GRTEL  ++
Sbjct: 243 LEFD-MTVHDVEHHRSVLLSVEGLTRQNNYKDVSFELHRGEILGITGLLGSGRTELALSL 301

Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358
           FG  P   G I +EGK + ++   D I  GIG V EDR  LG+++  SI  N  L  LDR
Sbjct: 302 FGKNPPDSGTIALEGKYLSLSSIRDGIYSGIGYVSEDRLTLGIVMDQSIRDNSVLTVLDR 361

Query: 359 IKK--GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416
           +K   G     KR+ +L   +++   ++ +  +  V  LSGGNQQKVVLAKWLA KPK+L
Sbjct: 362 LKSSFGTIDGTKRD-QLVSSSVQELSVKVSDVNLPVRTLSGGNQQKVVLAKWLATKPKVL 420

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476
           ILD PT G+D+ AK  IY I+  L+ +G+G+IMIS E+PEV     RI  M  G++ G  
Sbjct: 421 ILDSPTVGVDIAAKKGIYDIVKSLSAKGMGIIMISDEIPEVYYNCHRIITMQRGRITGEY 480

Query: 477 DAKEASQE 484
              E S++
Sbjct: 481 RPTETSEQ 488



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 74/245 (30%), Positives = 132/245 (53%), Gaps = 16/245 (6%)

Query: 258 LEVKNLSGERF------ENVSFSLRRGEILGFAGLVGAGRTELMETIFG-FRPKRGGEIY 310
           +E++N+S +RF      ++V  SL  GEI   AG  G+G++ L++ I G +RP+ G EI+
Sbjct: 8   IELRNIS-KRFGGVTALDDVGLSLSPGEIHCLAGQNGSGKSTLIKIISGVYRPEDGAEIF 66

Query: 311 IEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKRE 370
           I+G+ V ++ P  AI  GI ++ +D   L +   +S+  N+ L      +KG F   K  
Sbjct: 67  IDGELVALD-PAKAIGIGIQVIYQD---LSIFPGLSVAENIGLGQY--CEKGRFFVDKG- 119

Query: 371 KELADWAIKTFDIRPAYPDRK-VLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGA 429
           + ++D       I  + P RK V  LS  ++Q V + + LA   +++I+DEPT  +    
Sbjct: 120 RLVSDAKTAMNKIGISLPLRKKVSELSIADRQLVAICRALANDARLVIMDEPTASLTRTE 179

Query: 430 KAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKL 489
              +  ++ +L    + V+ +S  L EV+++++R+ V+  GK  G+ +A E   +K+   
Sbjct: 180 VKALLSVVKELKNRDIAVVFVSHRLDEVIEVAERVTVLRDGKSVGVFEASELDDKKLATY 239

Query: 490 AAGLE 494
             GLE
Sbjct: 240 MTGLE 244


Lambda     K      H
   0.318    0.138    0.385 

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: 626
Number of extensions: 39
Number of successful extensions: 9
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: 494
Length of database: 497
Length adjustment: 34
Effective length of query: 460
Effective length of database: 463
Effective search space:   212980
Effective search space used:   212980
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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