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 ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS06950 AZOBR_RS06950 ABC transporter

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__azobra:AZOBR_RS06950
          Length = 520

 Score =  253 bits (645), Expect = 2e-71
 Identities = 179/508 (35%), Positives = 265/508 (52%), Gaps = 25/508 (4%)

Query: 5   DSLSQGSP--LLTLSGIGKRYAAPVL-DGIDLDLRPGQVLALTGENGAGKSTLSKIICGL 61
           DS S  SP   L L GI KR+   +  D +DL LRPG++ AL GENGAGKSTL KII G+
Sbjct: 2   DSPSVSSPPHRLELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGV 61

Query: 62  VDASAGGMMLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWID 121
           + A AG +  +G          A  LGI MV Q  +L  TL++AEN+ L         +D
Sbjct: 62  LHADAGRIQWNGHDTHIPDPAGARRLGIGMVFQHFSLFDTLTVAENISLG--------LD 113

Query: 122 RKKLAEAARAQMEVV----GLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPT 177
           +    +A  A++  V    GL  LDP   V +L +G +Q VEI R L+   + LI+DEPT
Sbjct: 114 QPGPIDALSARIAEVSERYGLS-LDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPT 172

Query: 178 AMLTNREVELLFSRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYS 237
           ++LT +E   LF  + RL AEG  I+YISH+LEE++ + D   VLR G++V + D  R +
Sbjct: 173 SVLTPQEATRLFETLRRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRET 232

Query: 238 TEQLVQLMAGELTKVDLDAEHRRIGAPVLRIRGLGR------APVVHPASLALHAGEVLG 291
              L ++M G              GA  L++R L        A  +   S  + AGE+LG
Sbjct: 233 ARSLAEMMIGTELSTPERLPQGEAGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILG 292

Query: 292 IAGLIGSGRTELLRLIFGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQG 351
           IAG+ G+G+ EL+  + G +        +     PA    P++    G+A V E+R G+G
Sbjct: 293 IAGVAGNGQAELMAALSG-EALVPDPASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRG 351

Query: 352 LLLPQAISVNTSLANLG--SVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGG 409
            +   ++S N  L+      + R G++      S A+  +    + +      A  LSGG
Sbjct: 352 AVPELSLSENALLSGYAREPLVRSGLVHFGRARSYAERIIGAFNVVTHGHRAEARSLSGG 411

Query: 410 NQQKVVIARWLYRDCPIMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELM 469
           N QK +I R + +   +++  +PT G+D GA + I+R   +LA  G  +LV+S DL EL 
Sbjct: 412 NLQKFIIGREILQKPRLLVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELF 471

Query: 470 QICDRIAVMSAGRIADTFSRDDWSQERI 497
            + DRIAV+  G ++++      S E I
Sbjct: 472 VLSDRIAVLFHGHLSESRPTHHTSVEEI 499



 Score = 59.7 bits (143), Expect = 3e-13
 Identities = 61/232 (26%), Positives = 99/232 (42%), Gaps = 16/232 (6%)

Query: 28  LDGIDLDLRPGQVLALTGENGAGKSTLSKIICG--LVDASAGGMMLDGQPYAPASRTQAE 85
           L  +  ++R G++L + G  G G++ L   + G  LV   A  + ++G+P       +  
Sbjct: 278 LKDVSFEVRAGEILGIAGVAGNGQAELMAALSGEALVPDPAS-VAIEGRPAGHLGPRERR 336

Query: 86  GLGIRMVMQEL---NLIPTLSIAENLFLEKLPR----RFGWID---RKKLAEAARAQMEV 135
            LG+  V +E      +P LS++EN  L    R    R G +     +  AE       V
Sbjct: 337 LLGLAFVPEERLGRGAVPELSLSENALLSGYAREPLVRSGLVHFGRARSYAERIIGAFNV 396

Query: 136 VGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFSRIERL 195
           V  G          L  G+ Q   I R ++   R L++ +PT  +       +   +  L
Sbjct: 397 VTHGHR---AEARSLSGGNLQKFIIGREILQKPRLLVVGQPTWGVDAGAAAAIHRALIDL 453

Query: 196 RAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAG 247
              G A++ IS  L+EL  ++DRI VL  G L  +      S E++  LM G
Sbjct: 454 ARAGAAVLVISQDLDELFVLSDRIAVLFHGHLSESRPTHHTSVEEIGLLMGG 505


Lambda     K      H
   0.320    0.137    0.390 

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: 641
Number of extensions: 41
Number of successful extensions: 8
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: 522
Length of database: 520
Length adjustment: 35
Effective length of query: 487
Effective length of database: 485
Effective search space:   236195
Effective search space used:   236195
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 Apr 09 2024. 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 2024 update 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