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_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  384 bits (986), Expect = e-111
 Identities = 200/498 (40%), Positives = 320/498 (64%), Gaps = 8/498 (1%)

Query: 17  SSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS 76
           ++S P++A+R + K F GV ALD   F +  GE+HAL+GENGAGKSTL+K L+GVYQRD+
Sbjct: 7   TASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDA 66

Query: 77  GDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDE 136
           G + L+G+ +      +AQ L IG ++QE+NL+ +LS A+N+F+GR+P +  GL +D   
Sbjct: 67  GTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMR-FGL-VDRGA 124

Query: 137 LNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEI 196
           + R+A A+     L +D + P+G  +VA QQ+V IA+A+   ++VLI+DEPTA+L+  E+
Sbjct: 125 MRRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEV 184

Query: 197 AELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMM 256
           A LF+++R L+++G+GIV+++H +D++  + DR++V+R+G+ +      E     +++MM
Sbjct: 185 AVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMM 244

Query: 257 VGRALDG-EQRI--PPDTSRNDV---VLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGA 310
           +GR L+    RI  P D +  D    ++  RG  + R++      +R GE++G AGL+G+
Sbjct: 245 LGRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGS 304

Query: 311 GRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQA 370
           GRTE AR +FG D  + GE  + G    ++ P DA+  G G+  EDRK  G+   + V+ 
Sbjct: 305 GRTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRE 364

Query: 371 NIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWL 430
           NI L+   R   +  + +    E A  ++R L I+TP  EQ  +LLSGGNQQK ++A+WL
Sbjct: 365 NIILALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWL 424

Query: 431 LRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCE 490
             +  +L  DEPTRGIDVGA +EI +L++ L   G A++++SSEL E++  S RV+V+ +
Sbjct: 425 ATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRD 484

Query: 491 GRITGELARADATQEKIM 508
            R   EL   +   ++I+
Sbjct: 485 RRHVAELRGGEVAVDRIV 502



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 68/261 (26%), Positives = 131/261 (50%), Gaps = 16/261 (6%)

Query: 14  ASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQ 73
           A   +  P++  R   K      +++    ++  GEV  L G  G+G++   +++ G+ +
Sbjct: 263 AEEDARPPLVRFRGYGK----ARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDR 318

Query: 74  RDSGDILLDGKPVEITEPRQAQALGIGIIHQELN---LMNHLSAAQNIFIGREPRKAMGL 130
            D G+  +DG+ V +  PR A  LG G   ++     ++  LS  +NI +  + R+    
Sbjct: 319 ADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWLR 378

Query: 131 FIDEDELNRQAAAIFARMRLDMDPSTPVGE-----LTVARQQMVEIAKALSFDSRVLIMD 185
            I       + A  F R+   +D  TP  E     L+   QQ   +A+ L+ + R+LI+D
Sbjct: 379 PIPRCR-QEEIADRFIRL---LDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILD 434

Query: 186 EPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQ 245
           EPT  ++    AE+ R+I  L A G+ ++ +S +++E+   + RV V+RD +++A +   
Sbjct: 435 EPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGG 494

Query: 246 ETSMDTIISMMVGRALDGEQR 266
           E ++D I++ +   ++  E R
Sbjct: 495 EVAVDRIVAAIASESVPEEPR 515



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 63/251 (25%), Positives = 116/251 (46%), Gaps = 10/251 (3%)

Query: 269 PDTSRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADP 324
           P  + +  +L +RGL++     +A+  V FT+R GEI    G  GAG++ + + + G   
Sbjct: 4   PTPTASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQ 63

Query: 325 LEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG 384
            +AG + + G     +   +A    IG + ++     L   + V  N+ L       R G
Sbjct: 64  RDAGTVTLEGRAIAPRGVEEAQRLHIGTVYQE---VNLLPNLSVAENLFLGRQPM--RFG 118

Query: 385 FMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTR 444
            +D+ A+R  A+  +    + T  V       S   QQ + IA+ +     +L  DEPT 
Sbjct: 119 LVDRGAMRRRARAVLIPYGL-TLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTA 177

Query: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ 504
            +D    + ++K++  L  +G  IV ++  L +V  +  R+ V+  GR+ GE   A+  +
Sbjct: 178 SLDAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPR 237

Query: 505 EKIMQLATQRE 515
             ++ +   RE
Sbjct: 238 LDLVAMMLGRE 248


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: 671
Number of extensions: 38
Number of successful extensions: 8
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: 520
Length of database: 516
Length adjustment: 35
Effective length of query: 485
Effective length of database: 481
Effective search space:   233285
Effective search space used:   233285
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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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