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 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  327 bits (839), Expect = 5e-94
 Identities = 177/485 (36%), Positives = 285/485 (58%), Gaps = 10/485 (2%)

Query: 2   VSSTTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFG 61
           ++  TP++   LL + G++K+F GV+ALD V+  VR   IHAL+GENGAGKSTL+K L G
Sbjct: 1   MTDPTPTASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTG 60

Query: 62  IYQKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFV 121
           +YQ+D+GT+  +G+ I     +EA    I  V+QE+NL+   SV +N++LGR P +   V
Sbjct: 61  VYQRDAGTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLV 120

Query: 122 DQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
           D+  M R  +A+     + +D  A +G  SV+  Q++ IA+A   +AK++I+DEPT+SL 
Sbjct: 121 DRGAMRRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLD 180

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKI 241
            +EV  LF ++R L+ RG GIV+++H +++++ LCD +TVLR+G+ +     A L    +
Sbjct: 181 AQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDL 240

Query: 242 IAMMVGRSLN-------QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGI 294
           +AMM+GR L            D E      ++  R     R  S+     D+  GE++G+
Sbjct: 241 VAMMLGRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKAR--SVEPFDLDIRPGEVVGL 298

Query: 295 AGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYA 354
           AGL+G+ RT+    +FG+     G   + G+ +      +AI  GF    E+R+  GI  
Sbjct: 299 AGLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVG 358

Query: 355 YLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQK 414
            L +  N +++ ++  +  +  +   R +      I  + ++TP     I  LSGGNQQK
Sbjct: 359 ALSVRENIILA-LQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQK 417

Query: 415 VIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITD 474
            ++ RWL T+P +L+LDEPTRGIDVGA  EI +LI  L   G  ++++SSE+ E++  + 
Sbjct: 418 ALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSR 477

Query: 475 RILVM 479
           R++V+
Sbjct: 478 RVVVL 482



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 59/224 (26%), Positives = 107/224 (47%), Gaps = 9/224 (4%)

Query: 265 ILEVRNLTS--LRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITL 322
           +L +R L+   L   ++  V F +  GEI  + G  GA ++ +++TL G+ ++ AGT+TL
Sbjct: 12  LLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTL 71

Query: 323 HGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRM 382
            G+ I      EA       V +E     +   L +  N  +        + GL+D   M
Sbjct: 72  EGRAIAPRGVEEAQRLHIGTVYQE---VNLLPNLSVAENLFLGR---QPMRFGLVDRGAM 125

Query: 383 KSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAK 442
           +   + V+    + T      +G  S   QQ V I R +    ++L+LDEPT  +D    
Sbjct: 126 RRRARAVLIPYGL-TLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEV 184

Query: 443 FEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSG 486
             +++++  L  +G GI+ ++  + ++  + DRI V+ NG + G
Sbjct: 185 AVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVG 228



 Score = 65.1 bits (157), Expect = 6e-15
 Identities = 52/236 (22%), Positives = 107/236 (45%), Gaps = 6/236 (2%)

Query: 21  KSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFH 80
           + +   ++++  +L +RP  +  L G  G+G++   + +FG+ + D G     G+ +   
Sbjct: 275 RGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLR 334

Query: 81  SAKEALENGISMVHQELN---LVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAIFDEL 137
             ++A+  G     ++     +V   SV +N+ L     +G      +  +E  A     
Sbjct: 335 GPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWLRPIPRCRQEEIADRFIR 394

Query: 138 DIDI-DPRAR--VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRK 194
            +DI  P A   +  LS    Q   +A+  +   +++I+DEPT  +       +  +I +
Sbjct: 395 LLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIER 454

Query: 195 LKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250
           L   G  ++ +S ++EEI      V VLRD + +A      + +D+I+A +   S+
Sbjct: 455 LCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRIVAAIASESV 510


Lambda     K      H
   0.318    0.136    0.384 

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: 578
Number of extensions: 25
Number of successful extensions: 7
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: 516
Length adjustment: 35
Effective length of query: 471
Effective length of database: 481
Effective search space:   226551
Effective search space used:   226551
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:

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