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; EC 7.5.2.11 (characterized)
to candidate AZOBR_RS06950 AZOBR_RS06950 ABC transporter

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__azobra:AZOBR_RS06950
          Length = 520

 Score =  297 bits (760), Expect = 7e-85
 Identities = 187/508 (36%), Positives = 279/508 (54%), Gaps = 25/508 (4%)

Query: 3   STISPPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGI 62
           S  SPP   + LE+RGI K FPG  A D V+L +RP  IHAL+GENGAGKSTL+K ++G+
Sbjct: 5   SVSSPP---HRLELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGV 61

Query: 63  YQKDSGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVD 122
              D+G I + G +        A   GI MV Q  +L    +V +N+ LG        +D
Sbjct: 62  LHADAGRIQWNGHDTHIPDPAGARRLGIGMVFQHFSLFDTLTVAENISLG--------LD 113

Query: 123 Q----DKMYQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178
           Q    D +      + +   + +DPR  V  LSV + Q +EI +    + K++IMDEPTS
Sbjct: 114 QPGPIDALSARIAEVSERYGLSLDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTS 173

Query: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDM 238
            LT +E   LF  +R+L   GC I+YISHK+EEI  LCD  T+LR G+ + +        
Sbjct: 174 VLTPQEATRLFETLRRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETA 233

Query: 239 DKIIAMMVGRSLN--QRFPDKENKPGDVILEVRHLTSLRQ----PSIRDVSFDLHKGEIL 292
             +  MM+G  L+  +R P  E   G   L+VRHL++        +++DVSF++  GEIL
Sbjct: 234 RSLAEMMIGTELSTPERLPQGE--AGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEIL 291

Query: 293 GIAGLVGAKRTDIVETLFG-IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTG 351
           GIAG+ G  + +++  L G        ++ + G+   +    E    G A V EER   G
Sbjct: 292 GIAGVAGNGQAELMAALSGEALVPDPASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRG 351

Query: 352 IYAYLDIGFNSLISNI-RNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGG 410
               L +  N+L+S   R    + GL+   R +S  + +I +  V T GHR +  SLSGG
Sbjct: 352 AVPELSLSENALLSGYAREPLVRSGLVHFGRARSYAERIIGAFNVVTHGHRAEARSLSGG 411

Query: 411 NQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELL 470
           N QK IIGR +L +P +L++ +PT G+D GA   I++ + +LA+ G  +++IS ++ EL 
Sbjct: 412 NLQKFIIGREILQKPRLLVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELF 471

Query: 471 GITDRILVMSNGLVSGIVDTKTTTQNEI 498
            ++DRI V+ +G +S    T  T+  EI
Sbjct: 472 VLSDRIAVLFHGHLSESRPTHHTSVEEI 499



 Score = 60.1 bits (144), Expect = 2e-13
 Identities = 57/240 (23%), Positives = 110/240 (45%), Gaps = 17/240 (7%)

Query: 266 LEVRHLTSLRQPSIRDVSFDL--HKGEILGIAGLVGAKRTDIVETLFGIREKSSGTITLH 323
           LE+R +T      + +   DL    GEI  + G  GA ++ +V+ ++G+    +G I  +
Sbjct: 13  LELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWN 72

Query: 324 GKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLD--NSR 381
           G   +      A   G  +V +       ++  D    ++  NI    ++ G +D  ++R
Sbjct: 73  GHDTHIPDPAGARRLGIGMVFQH------FSLFDT--LTVAENISLGLDQPGPIDALSAR 124

Query: 382 MKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGA 441
           +   ++    S+       R  + +LS G +Q+V I R LL  P++L++DEPT  +    
Sbjct: 125 IAEVSERYGLSL-----DPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQE 179

Query: 442 KFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
              +++ +  LA +G  I+ IS ++ E+  + D   V+  G V G  D +  T   +  +
Sbjct: 180 ATRLFETLRRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARSLAEM 239



 Score = 50.8 bits (120), Expect = 1e-10
 Identities = 55/265 (20%), Positives = 110/265 (41%), Gaps = 18/265 (6%)

Query: 1   MGSTISPP-------SGEYLLEMRGINKSF--PGVKALDNVNLNVRPHSIHALMGENGAG 51
           +G+ +S P       +G   L++R ++ +   P    L +V+  VR   I  + G  G G
Sbjct: 241 IGTELSTPERLPQGEAGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILGIAGVAGNG 300

Query: 52  KSTLLKCLFG-IYQKDSGSIVFQGKEVDFHSAKEALENGISMVHQEL---NLVLQRSVMD 107
           ++ L+  L G     D  S+  +G+       +E    G++ V +E      V + S+ +
Sbjct: 301 QAELMAALSGEALVPDPASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRGAVPELSLSE 360

Query: 108 NMWLGRYPTKGM----FVDQDKMYQDTKAIFDELDIDIDP-RARVGTLSVSQMQMIEIAK 162
           N  L  Y  + +     V   +     + I    ++     RA   +LS   +Q   I +
Sbjct: 361 NALLSGYAREPLVRSGLVHFGRARSYAERIIGAFNVVTHGHRAEARSLSGGNLQKFIIGR 420

Query: 163 AFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITIL 222
                 +++++ +PT  +       +   +  L   G  ++ IS  ++E+F L D I +L
Sbjct: 421 EILQKPRLLVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELFVLSDRIAVL 480

Query: 223 RDGQWIATQPLEGLDMDKIIAMMVG 247
             G    ++P     +++I  +M G
Sbjct: 481 FHGHLSESRPTHHTSVEEIGLLMGG 505


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: 584
Number of extensions: 29
Number of successful extensions: 9
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: 520
Length adjustment: 35
Effective length of query: 471
Effective length of database: 485
Effective search space:   228435
Effective search space used:   228435
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 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