Alignments for a candidate for mglA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Azospirillum brasilense Sp245

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 AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  361 bits (927), Expect = e-104
 Identities = 200/498 (40%), Positives = 304/498 (61%), Gaps = 11/498 (2%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L ++ + K F GV AL GV      GE+HA++GENGAGKSTL+K + GVYQ D G + 
Sbjct: 11  PLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVT 70

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
            EGR +      EA    I TV+QE++++ NLSVAEN+F+G +  R   +D   M R A 
Sbjct: 71  LEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRAR 130

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
             +   +G+ +D    LG++S+A QQ+V IARAV   AKVLILDEPT+SL  +E   LF+
Sbjct: 131 AVLIP-YGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFK 189

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           V+++L+ +G+ I+F++H L++++ +CD+++VLR+G  +G      L +  +V MM+GR+L
Sbjct: 190 VMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGREL 249

Query: 243 EKFYIKEAHEPGEVVLEVKNLSGERF---------ENVSFSLRRGEILGFAGLVGAGRTE 293
           E    + A  P +   E       RF         E     +R GE++G AGL+G+GRTE
Sbjct: 250 EAVAHRIA-PPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTE 308

Query: 294 LMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSL 353
               +FG      GE  ++G+ V +  P DAI  G G  PEDRKK G++  +S+  N+ L
Sbjct: 309 TARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIIL 368

Query: 354 PSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP 413
               R      I   R++E+AD  I+  DIR  + ++ +  LSGGNQQK +LA+WLA +P
Sbjct: 369 ALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEP 428

Query: 414 KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLA 473
           ++LILDEPTRGIDVGA AEI R++ +L  +G+ ++++SSEL E++  S R+ V+   +  
Sbjct: 429 RLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHV 488

Query: 474 GIIDAKEASQEKVMKLAA 491
             +   E + ++++   A
Sbjct: 489 AELRGGEVAVDRIVAAIA 506



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 60/235 (25%), Positives = 111/235 (47%), Gaps = 12/235 (5%)

Query: 263 LSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPL 322
           L  +  + V F++R GEI    G  GAG++ L++T+ G   +  G + +EG+ +      
Sbjct: 23  LGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTLEGRAIAPRGVE 82

Query: 323 DAIEQGIGLVPEDRKKLGLILIMSIMHNVSL---PSLDRIKKGPFISFKREKELADWAIK 379
           +A    IG V ++   + L+  +S+  N+ L   P    +     +  +    L  + + 
Sbjct: 83  EAQRLHIGTVYQE---VNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRARAVLIPYGL- 138

Query: 380 TFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQ 439
           T D+        V       QQ V +A+ + +  K+LILDEPT  +D    A ++++M  
Sbjct: 139 TLDVTAPLGRFSV-----ATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKVMRT 193

Query: 440 LAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           L   G+G++ ++  L +V  + DRI V+  G+L G     E  +  ++ +  G E
Sbjct: 194 LRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGRE 248


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: 622
Number of extensions: 32
Number of successful extensions: 8
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: 516
Length adjustment: 34
Effective length of query: 460
Effective length of database: 482
Effective search space:   221720
Effective search space used:   221720
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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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 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