Alignments for a candidate for rbsA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Azospirillum brasilense Sp245

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  359 bits (922), Expect = e-103
 Identities = 199/495 (40%), Positives = 303/495 (61%), Gaps = 10/495 (2%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           LL ++G+ KAF GV+AL G    V  G + AL+GENGAGKST++K LTG+Y RDAGT+  
Sbjct: 12  LLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTL 71

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            G+     G + +Q   IG ++QE+NL+P L++AEN+FLGR+ + RFG +D   M   A 
Sbjct: 72  EGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPM-RFGLVDRGAMRRRAR 130

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
            +L    L       +G  S+  QQ+V IA+ +   +KV+I+DEPT +L   E   LF+V
Sbjct: 131 AVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKV 190

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
           +R L+S+G GIV+++H + +++ +CD +TV R+G+ + ER  A L    L+ MM+GR+LE
Sbjct: 191 MRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGRELE 250

Query: 244 DQY----PHLDKAPGDIRLKVDNLCGPG----VNDVSFTLRKGEILGVSGLMGAGRTELM 295
                  P  D A  D R  +    G G    V      +R GE++G++GL+G+GRTE  
Sbjct: 251 AVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETA 310

Query: 296 KVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTA 355
           ++++G      G   +DG  V  R P+D +  G  +  EDRK++G+V  +SV+EN+ L A
Sbjct: 311 RLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIIL-A 369

Query: 356 LRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPK 415
           L+        +    +++    FIRL +++TP  EQ I LLSGGNQQK  +AR L T P+
Sbjct: 370 LQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPR 429

Query: 416 VLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSG 475
           +LILDEPTRG+DVGA  EI +LI +  ADG+++++VSSE+ E++  S R++V+ +     
Sbjct: 430 LLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVA 489

Query: 476 EFTREQATQEVLMAA 490
           E    +   + ++AA
Sbjct: 490 ELRGGEVAVDRIVAA 504



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 71/231 (30%), Positives = 117/231 (50%), Gaps = 15/231 (6%)

Query: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDG--L 325
           ++ V FT+R GEI  + G  GAG++ L+K L G   R +G VTL+G  +  R  ++   L
Sbjct: 28  LDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTLEGRAIAPRGVEEAQRL 87

Query: 326 ANGIVYISEDRKRDGLVLGMSVKENMSL--TALRYFSRAGGSLKHADEQQAVSDFIRLFN 383
             G VY     +   L+  +SV EN+ L    +R+     G+++       +   + L +
Sbjct: 88  HIGTVY-----QEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRARAVLIPYGLTL-D 141

Query: 384 VKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKA 443
           V  P     +G  S   QQ VAIAR +    KVLILDEPT  +D      +++++   ++
Sbjct: 142 VTAP-----LGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKVMRTLRS 196

Query: 444 DGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            G+ I+ V+  + +V  + DRI V+  G L GE    +  +  L+A  +G+
Sbjct: 197 RGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGR 247



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 57/247 (23%), Positives = 120/247 (48%), Gaps = 9/247 (3%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           L++ +G  KA    +++    L++ PG V+ L G  G+G++   +++ G+   D G    
Sbjct: 271 LVRFRGYGKA----RSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAAV 326

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELN---LIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120
            G+     GP+ +   G G   ++     ++  L++ ENI L  +    + +   +    
Sbjct: 327 DGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWLRPIPRCRQE 386

Query: 121 E-ADKLLAKLNLRFK-SDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETE 178
           E AD+ +  L++R   +++ +  LS G+QQ   +A+ L+ E +++I+DEPT  +      
Sbjct: 387 EIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGAHA 446

Query: 179 SLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMV 238
            + R+I  L + G  ++ +S  ++EI      V V RD + +AE     +  D ++  + 
Sbjct: 447 EIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRIVAAIA 506

Query: 239 GRKLEDQ 245
              + ++
Sbjct: 507 SESVPEE 513


Lambda     K      H
   0.318    0.137    0.380 

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: 643
Number of extensions: 37
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: 501
Length of database: 516
Length adjustment: 34
Effective length of query: 467
Effective length of database: 482
Effective search space:   225094
Effective search space used:   225094
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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