GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Desulfovibrio vulgaris Hildenborough

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 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  297 bits (760), Expect = 7e-85
 Identities = 161/482 (33%), Positives = 280/482 (58%), Gaps = 6/482 (1%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P++ ++ I K F  V A   ++++  PG + A++GENGAGKSTLM I++G    D G I 
Sbjct: 33  PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
            +G  VR+  P +A+ AGI  V+Q   ++D+++VAEN+ +G     G ++    M R   
Sbjct: 93  VDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS---GAWLSPVHMSRVVA 149

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           + +   +G++IDP  ++   S+  +Q VEI + +Y+ ++VLILDEPT+ LT  ETE+LFE
Sbjct: 150 E-LAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFE 208

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKE-KIVEMMVGRK 241
            +  + E G AI+FISH+++E+  + D++++LR GE +       +  E ++   MVGR+
Sbjct: 209 ALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGRE 268

Query: 242 LEKFYIKEAHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301
           +      E  EPG+ VL V  L+G+  + +SF +R+GE+   AG+ G G+ EL+E + G 
Sbjct: 269 VILEVAAEPLEPGDRVLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGL 328

Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361
           R    GE+ + G            + G+  +PEDR+ L   L + ++ N  L +     +
Sbjct: 329 RRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTR 388

Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421
           GPF+  K     A   +  ++++P   +     LSGGN QK+V+ +    KP +++ + P
Sbjct: 389 GPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENP 448

Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481
           T+G+D+ A  E++  + ++ +   GV+++S +L EVL ++DR+AVM  G   G++D  + 
Sbjct: 449 TQGLDIAATEEVWARLLEV-RSHAGVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDT 507

Query: 482 SQ 483
           ++
Sbjct: 508 NK 509



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 62/217 (28%), Positives = 112/217 (51%), Gaps = 13/217 (5%)

Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329
           +++  +  G I    G  GAG++ LM  + G   +  G I+++G+ V    P DA++ GI
Sbjct: 52  DITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGI 111

Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFIS-FKREKELADWAIKT-FDIRPAY 387
           G+V +      L+  M++  NV L      + G ++S     + +A+ A +   DI PA 
Sbjct: 112 GMVYQH---FMLVDSMTVAENVLLG-----QSGAWLSPVHMSRVVAELAARYGLDIDPA- 162

Query: 388 PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGV 447
              +V  LS G +Q+V + K L    ++LILDEPT  +  G   +++  + ++A+ G  +
Sbjct: 163 --ARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAI 220

Query: 448 IMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQE 484
           + IS ++ EVL ++D IA++  G++       E   E
Sbjct: 221 VFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGE 257



 Score = 69.7 bits (169), Expect = 2e-16
 Identities = 58/226 (25%), Positives = 101/226 (44%), Gaps = 10/226 (4%)

Query: 20  LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNH-----PS 74
           LKG+S E   GEV AI G  G G+  L++ + G+ +P EGE+  E  G+ W       P 
Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEV--ELLGIPWRQFFTKAPR 352

Query: 75  EAINAGIVTVFQELSVMDNLSVAENIFMGDEE--KRGIFIDYKKMYREAEKFMKEEFGIE 132
           +   A I    Q L+   +L + +N  +       RG F+D K     A   + E     
Sbjct: 353 QGGLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQP 412

Query: 133 IDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGV 192
              E      S    Q + + R  Y+K  +++ + PT  L    TE+++  +  ++    
Sbjct: 413 GRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA- 471

Query: 193 AIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
            ++ +S  L E+  + D+V+V+  G +IG     +  K   + +M+
Sbjct: 472 GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMM 517


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: 614
Number of extensions: 30
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 494
Length of database: 524
Length adjustment: 34
Effective length of query: 460
Effective length of database: 490
Effective search space:   225400
Effective search space used:   225400
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 17 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