Alignments for a candidate for xylK_Tm in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Azospirillum brasilense Sp245

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS06950 AZOBR_RS06950 ABC transporter

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__azobra:AZOBR_RS06950
          Length = 520

 Score =  283 bits (725), Expect = 8e-81
 Identities = 173/488 (35%), Positives = 268/488 (54%), Gaps = 26/488 (5%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L+ +GI KRFPG +A D VD  +   EI +L+GENGAGKSTL+KI+ GVL  DAG I  N
Sbjct: 13  LELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWN 72

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
           G       P  A + GI ++ Q  +L D +TVAENI L  +   G    LS+R+      
Sbjct: 73  GHDTHIPDPAGARRLGIGMVFQHFSLFDTLTVAENISLGLDQ-PGPIDALSARI------ 125

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
               E+ +  G    P   V NL+  +RQ VEI + L+++P+++ MDEPTS LT +E  R
Sbjct: 126 ---AEVSERYGLSLDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATR 182

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254
           LFE +  L + G +++++SH+L+E+  + D   V+R G+ +G          ++ +MM+G
Sbjct: 183 LFETLRRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARSLAEMMIG 242

Query: 255 REV---EFFPHGIETRPGEIALEVRNLK------WKDKVKNVSFEVRKGEVLGFAGLVGA 305
            E+   E  P G     G   L+VR+L       +   +K+VSFEVR GE+LG AG+ G 
Sbjct: 243 TELSTPERLPQG---EAGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILGIAGVAGN 299

Query: 306 GRTETMLLVFG-VNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVK 364
           G+ E M  + G     +   + + GR      P +   +G+  +PE+R  +G V  +++ 
Sbjct: 300 GQAELMAALSGEALVPDPASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRGAVPELSLS 359

Query: 365 DNIVLPSLKK--ISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVL 422
           +N +L    +  + R GLV   R     +E  +   ++ T        +LSGGN QK ++
Sbjct: 360 ENALLSGYAREPLVRSGLVHFGR-ARSYAERIIGAFNVVTHGHRAEARSLSGGNLQKFII 418

Query: 423 AKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIV 482
            + +     +L+  +PT G+D GA A IHR + +LA  G AV++IS +L E+  LSDRI 
Sbjct: 419 GREILQKPRLLVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELFVLSDRIA 478

Query: 483 VMWEGEIT 490
           V++ G ++
Sbjct: 479 VLFHGHLS 486



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 62/225 (27%), Positives = 101/225 (44%), Gaps = 37/225 (16%)

Query: 287 VSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIG 346
           V   +R GE+    G  GAG++  + +++GV   ++G I  NG    I +P  A ++GIG
Sbjct: 31  VDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWNGHDTHIPDPAGARRLGIG 90

Query: 347 LIPEDRKLQGLVLRMTVKDNIVL------------PSLKKIS-RWGLVLDERKEEEISED 393
           ++ +   L      +TV +NI L              + ++S R+GL LD R+       
Sbjct: 91  MVFQHFSLFDT---LTVAENISLGLDQPGPIDALSARIAEVSERYGLSLDPRRH------ 141

Query: 394 YVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRM 453
                            NLS G +Q+V + + L  +  +LI DEPT  +       +   
Sbjct: 142 ---------------VHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFET 186

Query: 454 IRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLDNREK 498
           +R LAA+G  ++ IS +L EI  L D   V+  G +    D R +
Sbjct: 187 LRRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRE 231


Lambda     K      H
   0.319    0.138    0.381 

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: 645
Number of extensions: 34
Number of successful extensions: 9
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: 520
Length adjustment: 35
Effective length of query: 485
Effective length of database: 485
Effective search space:   235225
Effective search space used:   235225
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 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