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_RS31880 AZOBR_RS31880 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__azobra:AZOBR_RS31880
          Length = 515

 Score =  284 bits (727), Expect = 5e-81
 Identities = 171/499 (34%), Positives = 276/499 (55%), Gaps = 21/499 (4%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L+  GI KRF  +VA D++   +++ E+++L+GENGAGK+TL+ IL G    D G I  
Sbjct: 7   VLRLSGITKRFGPLVANDSISLTLHKGEVLALLGENGAGKTTLMNILFGHYVADEGSIEA 66

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G+ +   SP  A   GI ++HQ   L DN++V +NI +  E++    R  S R      
Sbjct: 67  FGQPLPPGSPRAALAAGIGMVHQHFTLADNLSVLDNIAVGTESLW---RPRSDRA----- 118

Query: 134 YTRSKELLDL---IGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVE 190
                +LLDL    G +  PDALV +L+  +RQ  EI KAL ++ R++ +DEPT+ LT +
Sbjct: 119 -AAKAKLLDLARRFGLEVRPDALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQ 177

Query: 191 ETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIK 250
           E+  LF+ +  L + G++VVF+SH+++EV   SD + V+R G+ +   K  E D + + +
Sbjct: 178 ESASLFDTLRRLTADGLAVVFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAE 237

Query: 251 MMVGREVEFFPHGIETRPGEIALEVRNL-----KWKDKVKNVSFEVRKGEVLGFAGLVGA 305
           +MVGR ++  P      PGE  L +  +       +  +  V   VR+ +++G AG+ G 
Sbjct: 238 LMVGRALK-PPTPTPLEPGEPVLTLSGVTVASGHGRPLLDGVDLTVRRRQIVGIAGVSGN 296

Query: 306 GRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKD 365
           G+T    L+ G+   +SG + + G  +    P + ++ G+  IPEDR   GLV  M V +
Sbjct: 297 GQTALAELISGLIHPDSGTMTLKGEAIGNAEPAEMVRRGVARIPEDRHAAGLVGAMAVWE 356

Query: 366 NIVLPSL--KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLA 423
           N++          R+GL+         +E+ +    ++ P     T+ LSGGN QK++L 
Sbjct: 357 NLIAERYHDPAFQRFGLI-RRGAARAYAEEVIAAFDVRCPGPDARTQLLSGGNMQKLILG 415

Query: 424 KWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVV 483
           + LA   D+++  +PTRG+DVGA + +H  + E  A G  V++IS +L EIL L+D I V
Sbjct: 416 RTLAHGPDLILASQPTRGLDVGAVSYVHGRLLEARAAGAGVLVISEDLDEILALADGITV 475

Query: 484 MWEGEITAVLDNREKRVTQ 502
            + G +T VL +    V Q
Sbjct: 476 AYHGRLTPVLPHGRVSVRQ 494



 Score = 74.7 bits (182), Expect = 8e-18
 Identities = 56/230 (24%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 30  VDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKK 89
           +D VD  V   +IV + G +G G++ L ++++G++ PD+G + + GE +    P +  ++
Sbjct: 275 LDGVDLTVRRRQIVGIAGVSGNGQTALAELISGLIHPDSGTMTLKGEAIGNAEPAEMVRR 334

Query: 90  GISVIHQELN---LCDNMTVAENIFLA-YEAVRGQKRTLSSRVDENYMYTRSKELLDLIG 145
           G++ I ++ +   L   M V EN+    Y     Q+  L  R         ++E++    
Sbjct: 335 GVARIPEDRHAAGLVGAMAVWENLIAERYHDPAFQRFGLIRR---GAARAYAEEVIAAFD 391

Query: 146 AKF-SPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKS 204
            +   PDA  + L+    Q + + + L   P +I   +PT  L V     +   +   ++
Sbjct: 392 VRCPGPDARTQLLSGGNMQKLILGRTLAHGPDLILASQPTRGLDVGAVSYVHGRLLEARA 451

Query: 205 RGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254
            G  V+ +S  LDE++ ++D I V   G+    L  G   V  +  +M G
Sbjct: 452 AGAGVLVISEDLDEILALADGITVAYHGRLTPVLPHGRVSVRQLGLLMAG 501


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: 662
Number of extensions: 32
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: 520
Length of database: 515
Length adjustment: 35
Effective length of query: 485
Effective length of database: 480
Effective search space:   232800
Effective search space used:   232800
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 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