GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Tistlia consotensis USBA 355

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  318 bits (814), Expect = 4e-91
 Identities = 169/488 (34%), Positives = 285/488 (58%), Gaps = 2/488 (0%)

Query: 13  LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72
           LLE+RG+++ FPGV ALD V+  +RP  +H L GENGAGKST++  + G  +   G   F
Sbjct: 23  LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82

Query: 73  QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 132
           +G+ V+ +S   A   GIS V QE +LV Q +V +N++LG   T+   +D+  ++    A
Sbjct: 83  RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRADA 142

Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192
           I   L   + PR RV  L+ ++ QM+EIAKAF     ++I+DEPT+SLTE+E   LF +I
Sbjct: 143 ILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLI 202

Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLNQ 252
            ++K +G G++YI+H++ EI ++ D IT+LRDG+++AT   +     +++ +M GR  ++
Sbjct: 203 EQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRVYDE 262

Query: 253 RFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGI 312
            FP    KPG  +L V  LT+    S+ + S  +  GEI+G+AGLVG+ ++++    FG+
Sbjct: 263 LFPKVRFKPGRELLSVERLTT-ASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGL 321

Query: 313 REKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKN 372
            + + G + L G+++        +  GF  V  +RR  G+     +  N  + ++     
Sbjct: 322 EKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLAPF 381

Query: 373 KVGLLDNSRMKSD-TQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
             G L + R ++D  + + + + ++ P     + + SGGNQQKV++ +      ++   D
Sbjct: 382 GNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFD 441

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EPT G+DVG +  IY+ I +L + G GI++ISS++PE+L +++R  V   G V   +   
Sbjct: 442 EPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELAGD 501

Query: 492 TTTQNEIL 499
             T+ ++L
Sbjct: 502 EITEEKVL 509



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 60/244 (24%), Positives = 114/244 (46%), Gaps = 11/244 (4%)

Query: 261 PGDVILEVRHLTSLRQPSIR---DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSS 317
           P   +LE+R + S R P +     V F L  GE+  + G  GA ++ ++  + G    S 
Sbjct: 19  PAAPLLELRGV-SRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSE 77

Query: 318 GTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLL 377
           G     G+ +  ++ + A   G + V +E     +   + +  N  +        ++GLL
Sbjct: 78  GEFRFRGEPVELNSVHHARGLGISAVFQE---FSLVPQMTVEENLFLGA---ESTRLGLL 131

Query: 378 DNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGI 437
           D   +      ++  +       R ++  L+   QQ V I +   ++  +L+LDEPT  +
Sbjct: 132 DRRALHDRADAILKRLGFPLRP-RDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASL 190

Query: 438 DVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNE 497
                 ++++LI ++  +G G+I I+  + E+  I DRI V+ +G     VD +TT + E
Sbjct: 191 TERETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGE 250

Query: 498 ILRL 501
           ++RL
Sbjct: 251 LVRL 254



 Score = 58.5 bits (140), Expect = 5e-13
 Identities = 52/220 (23%), Positives = 98/220 (44%), Gaps = 10/220 (4%)

Query: 33  NLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVFQGKEVDFHSAKEALENGISM 92
           +L+V    I  L G  G+GKS + +  FG+ +   G +  +G+EV     K  L+ G   
Sbjct: 292 SLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFY 351

Query: 93  V---HQELNLVLQRSVMDNMWLGRYPT----KGMFVDQDKMYQDTKAIFDELDIDIDPRA 145
           V    ++  L++ R V +N+ L          G  +D+       + + ++L++   PR 
Sbjct: 352 VPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGALLDRRGETDRVRRLAEQLNLQ-PPRI 410

Query: 146 R--VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIV 203
              V   S    Q + +AK+ +   ++   DEPT  +       ++  IR L E G GI+
Sbjct: 411 ERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGIL 470

Query: 204 YISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIA 243
            IS  + E+  L +   +   G+  A    + +  +K+++
Sbjct: 471 LISSDLPEVLNLSNRAYVFYRGRVQAELAGDEITEEKVLS 510


Lambda     K      H
   0.319    0.137    0.388 

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: 518
Number of extensions: 18
Number of successful extensions: 6
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: 506
Length of database: 518
Length adjustment: 35
Effective length of query: 471
Effective length of database: 483
Effective search space:   227493
Effective search space used:   227493
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 (21.7 bits)
S2: 52 (24.6 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