Alignments for a candidate for PS417_12065 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Azospirillum brasilense Sp245

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  314 bits (805), Expect = 4e-90
 Identities = 180/482 (37%), Positives = 274/482 (56%), Gaps = 7/482 (1%)

Query: 2   ARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAG 61
           A P LL    ++KA+ GV AL     ++R G +HAL G NGAGKST +  L G+ QRDAG
Sbjct: 8   ASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAG 67

Query: 62  SILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALN 121
           ++ L G  +      EA    I  + QE+  +P ++VAEN++LGR+P R G +VD  A+ 
Sbjct: 68  TVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFG-LVDRGAMR 126

Query: 122 RRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQT 181
           RR R +L      +D T+P+ R SVA  Q+V IA+A     +V+I+DEPT+++   E   
Sbjct: 127 RRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAV 186

Query: 182 LFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241
           LFK +R L ++G GIV+V+H L ++  + D  ++ R+G  V   R A++ R  LV  ++G
Sbjct: 187 LFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLG 246

Query: 242 QELTRIDHKVG------RECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGR 295
           +EL  + H++        E A    ++     +A       L +R GE++G+ GL+GSGR
Sbjct: 247 RELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSGR 306

Query: 296 SEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNI 355
           +E    ++G+  AD G   + G+ + +  P+  I  G     EDRK  G+V   S+  NI
Sbjct: 307 TETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENI 366

Query: 356 ALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLST 415
            L+   R      I   ++ ++A+  ++ L I+T   E P+  +SGGNQQK +LA+ L+T
Sbjct: 367 ILALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLAT 426

Query: 416 EPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGR 475
           EP  L+ DEPTRGID GA  EI  L+++    G A +VVSSE  E++  S R+ V +  R
Sbjct: 427 EPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRR 486

Query: 476 LV 477
            V
Sbjct: 487 HV 488



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 62/252 (24%), Positives = 111/252 (44%), Gaps = 17/252 (6%)

Query: 2   ARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAG 61
           ARP L++     KA +  P      L +R G V  L G  G+G++    ++ G+ + D G
Sbjct: 267 ARPPLVRFRGYGKARSVEPF----DLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRG 322

Query: 62  SILLNGAPVQFNRPSEALAAGIAMITQELEP---IPYMTVAENIWLGREPRRAGCIVDNK 118
              ++G  V+   P +A+  G     ++ +    +  ++V ENI L  + R+       +
Sbjct: 323 EAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWL----R 378

Query: 119 ALNR-RTRELLDSLEFDVD-----ATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTS 172
            + R R  E+ D     +D     A  P+  LS    Q   +A+  + + +++I+DEPT 
Sbjct: 379 PIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTR 438

Query: 173 AIGEHEAQTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDR 232
            I       + + I RL A G  ++ VS  L E+   +    + RD   V   R  ++  
Sbjct: 439 GIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAV 498

Query: 233 DHLVRGIVGQEL 244
           D +V  I  + +
Sbjct: 499 DRIVAAIASESV 510


Lambda     K      H
   0.319    0.135    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: 573
Number of extensions: 30
Number of successful extensions: 7
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: 495
Length of database: 516
Length adjustment: 34
Effective length of query: 461
Effective length of database: 482
Effective search space:   222202
Effective search space used:   222202
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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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