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_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__azobra:AZOBR_RS31245
          Length = 518

 Score =  307 bits (787), Expect = 5e-88
 Identities = 181/500 (36%), Positives = 290/500 (58%), Gaps = 17/500 (3%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDA--GSI 63
           +L+ + + K + GV AL D  LS+R G +HAL G NGAGKST + +L G+  + +  G I
Sbjct: 5   ILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGEI 64

Query: 64  LLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRR 123
              G P  F   +++   GI +I QEL  +P +++ EN++LG E    G ++D  A   R
Sbjct: 65  RFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRG-VIDWDAATLR 123

Query: 124 TRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLF 183
            RELL  +       + +  + V + QLVEIAKA S + +++I+DEPT+++ E ++  L 
Sbjct: 124 ARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDALL 183

Query: 184 KAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVES--GRMADIDRDHLVRGIVG 241
           + + +  A+G   + +SH+L+E+A++AD  +I RDG  VE+   R A + +D ++RG+VG
Sbjct: 184 ELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMVG 243

Query: 242 QELTRIDHKVGRECAANTCL------QVDNLSRAGE--FHDISLQLRQGEILGIYGLMGS 293
           + L+  D    R       L        D+ +  G     D++L +R+GE++GI GLMG+
Sbjct: 244 RALS--DRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGA 301

Query: 294 GRSEFLNCIYGLTVADS--GSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSI 351
           GR+EF   ++G +   +  G   L G+ + +      +  G++  TEDRK  GLVL   I
Sbjct: 302 GRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDI 361

Query: 352 LSNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAK 411
             N+ L+  + ++   +I+  +E Q+AE+  +RL+I+   +     ++SGGNQQKVVL+K
Sbjct: 362 RHNVTLANLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLSK 421

Query: 412 CLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVF 471
            L  +P  L+ DEPTRGID GAK EIY +++Q V  G   +++SSE PELL ++DRI V 
Sbjct: 422 WLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYVM 481

Query: 472 KGGRLVTISTDTALSQEALL 491
             G +V        SQE ++
Sbjct: 482 NAGEMVAEMPAAEASQEKIM 501



 Score = 71.6 bits (174), Expect = 6e-17
 Identities = 60/233 (25%), Positives = 105/233 (45%), Gaps = 7/233 (3%)

Query: 15  AYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGIT--QRDAGSILLNGAPVQF 72
           A+ G   +RD  L++R G V  + G  GAG++ F   L G +  +   G   L+G  +  
Sbjct: 273 AHPGRRVVRDVNLTVRRGEVVGIAGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDV 332

Query: 73  NRPSEALAAGIAMITQELEPIPYMT---VAENIWLGREPRRAG-CIVDNKALNRRTRELL 128
           +  S A+A G+A  T++ + +  +    +  N+ L      A   ++D++   +   E  
Sbjct: 333 STISRAMANGLAYATEDRKHLGLVLDNDIRHNVTLANLRGVAKRWVIDHEREVQVAEEFR 392

Query: 129 DSLEFD-VDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIR 187
             L     D       LS    Q V ++K    D QV+I+DEPT  I       ++  I 
Sbjct: 393 RRLRIRCADVFQETVNLSGGNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIIN 452

Query: 188 RLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240
           +L A+G G+V +S  + EL  +AD   +   G  V     A+  ++ ++  I+
Sbjct: 453 QLVAEGRGVVLISSEMPELLGVADRIYVMNAGEMVAEMPAAEASQEKIMGAIM 505


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: 616
Number of extensions: 28
Number of successful extensions: 11
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: 518
Length adjustment: 34
Effective length of query: 461
Effective length of database: 484
Effective search space:   223124
Effective search space used:   223124
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