Alignments for a candidate for HSERO_RS05250 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Azospirillum brasilense Sp245

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__azobra:AZOBR_RS31245
          Length = 518

 Score =  379 bits (972), Expect = e-109
 Identities = 211/504 (41%), Positives = 322/504 (63%), Gaps = 18/504 (3%)

Query: 19  SVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS-- 76
           ++P++ ++ + K FPGV ALD+    +  GE+HAL+GENGAGKSTLMK+LSGVY + S  
Sbjct: 2   AMPILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFD 61

Query: 77  GDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDE 136
           G+I   G+P        ++ LGI IIHQEL L+  LS  +N+F+G E  +A    ID D 
Sbjct: 62  GEIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNE--QASRGVIDWDA 119

Query: 137 LNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEI 196
              +A  +   + L   P T + ++ V +QQ+VEIAKALS + ++LI+DEPTA+LN ++ 
Sbjct: 120 ATLRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDS 179

Query: 197 AELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQET--SMDTIIS 254
             L  ++   +A+G+  + ISHK++E+ ++ADRV+++RDG  + T+  +E   S D II 
Sbjct: 180 DALLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIR 239

Query: 255 MMVGRALDGEQRIPPDTS-RNDVVLEVRGLNRG-------RAIRDVSFTLRKGEILGFAG 306
            MVGRAL    R P  T+   DV+ EV+G +         R +RDV+ T+R+GE++G AG
Sbjct: 240 GMVGRALS--DRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAG 297

Query: 307 LMGAGRTEVARAIFGADPLE--AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAV 364
           LMGAGRTE A ++FG        G+  + G +  + + + A+A+G+ Y +EDRKH GL +
Sbjct: 298 LMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVL 357

Query: 365 GMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKI 424
             D++ N+ L+++    +   +D     + A+ + R+L I+   V Q+   LSGGNQQK+
Sbjct: 358 DNDIRHNVTLANLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKV 417

Query: 425 VIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHR 484
           V++KWL  D  +L  DEPTRGIDVGAK EIY +++ L  +G+ +V+ISSE+PE+L ++ R
Sbjct: 418 VLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADR 477

Query: 485 VLVMCEGRITGELARADATQEKIM 508
           + VM  G +  E+  A+A+QEKIM
Sbjct: 478 IYVMNAGEMVAEMPAAEASQEKIM 501



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 71/244 (29%), Positives = 116/244 (47%), Gaps = 8/244 (3%)

Query: 33  PGVLALDNCQFELAAGEVHALMGENGAGKSTL-MKILSGVYQRD-SGDILLDGKPVEITE 90
           PG   + +    +  GEV  + G  GAG++   M +    Y R+  G   LDG+ ++++ 
Sbjct: 275 PGRRVVRDVNLTVRRGEVVGIAGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVST 334

Query: 91  PRQAQALGIGIIHQE---LNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFAR 147
             +A A G+    ++   L L+       N+ +      A    ID +   + A     R
Sbjct: 335 ISRAMANGLAYATEDRKHLGLVLDNDIRHNVTLANLRGVAKRWVIDHEREVQVAEEFRRR 394

Query: 148 MRLDM-DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDL 206
           +R+   D       L+   QQ V ++K L  D +VLI+DEPT  ++     E++ II  L
Sbjct: 395 LRIRCADVFQETVNLSGGNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQL 454

Query: 207 QAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIIS--MMVGRALDGE 264
            A+G G+V IS +M EL  +ADR+ VM  G+ +A +P  E S + I+   M  G  L   
Sbjct: 455 VAEGRGVVLISSEMPELLGVADRIYVMNAGEMVAEMPAAEASQEKIMGAIMRSGETLMSG 514

Query: 265 QRIP 268
           + +P
Sbjct: 515 EALP 518


Lambda     K      H
   0.320    0.135    0.372 

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: 654
Number of extensions: 33
Number of successful extensions: 10
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: 520
Length of database: 518
Length adjustment: 35
Effective length of query: 485
Effective length of database: 483
Effective search space:   234255
Effective search space used:   234255
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 (21.8 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