GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtrB in Azospirillum brasilense Sp245

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate AZOBR_RS20015 AZOBR_RS20015 C4-dicarboxylate ABC transporter

Query= TCDB::P74224
         (445 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS20015 AZOBR_RS20015
           C4-dicarboxylate ABC transporter
          Length = 503

 Score =  504 bits (1297), Expect = e-147
 Identities = 245/443 (55%), Positives = 336/443 (75%), Gaps = 13/443 (2%)

Query: 7   LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGT 66
           + P+MF   ++FL  G+PVAF+L    +LF +IG  LG   P    A+P+R+FGIM N T
Sbjct: 9   MAPLMFAALVLFLLMGFPVAFALAANGLLFGLIGIELGLLTPALFQALPERVFGIMRNDT 68

Query: 67  LLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATV 126
           LLAIPFF F+G +LERSG+AE LL+T+G + G LRGGLA AVI VG +LAATTGVVAA+V
Sbjct: 69  LLAIPFFTFMGLILERSGMAEDLLDTVGQLFGPLRGGLAYAVIFVGALLAATTGVVAASV 128

Query: 127 VAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSL 186
           ++MGLISLPIMLRYGY + LASGVI ASGTL QIIPPS+VLI+LADQLG SVGD++ G+L
Sbjct: 129 ISMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIILADQLGRSVGDMYAGAL 188

Query: 187 LPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVLG 246
           +PGL++ G +A Y+L+++ ++P+  PALP E R++ G +L  R++  ++PPLVLI LVLG
Sbjct: 189 VPGLVLTGLYAGYILVVSIVRPEFTPALPPEARSLRGFQLLFRVLTSLVPPLVLIFLVLG 248

Query: 247 SIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFS 306
           +IF GIA+PTE GA+G+ GA+ LA   ++L+W  + +  D T +++S V+ IL+GST F 
Sbjct: 249 TIFIGIATPTEGGAMGAAGAMILALMKRQLSWSLMRQAMDTTAKLSSFVIFILIGSTVFG 308

Query: 307 LVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEA 366
           LVFR + GD ++  LL +LPGG++GFL +  I +F+L FF+DFFE+AFI++PL  PVAE 
Sbjct: 309 LVFRAVNGDLWVEHLLTSLPGGELGFLIVVNIMVFLLAFFLDFFELAFIIVPLLAPVAEK 368

Query: 367 LNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAP-------------ASLTTGQIYR 413
           L +DLIW+GV++G N+QTSF+ PPFGFALF+LR VAP               +TTGQIY 
Sbjct: 369 LGIDLIWFGVLLGVNMQTSFMHPPFGFALFFLRSVAPREDYKDKITGKIIKKITTGQIYW 428

Query: 414 GAVPFIGLQVLVLLLIIIFPALI 436
           GAVPF+ +Q++++ L+I+FP ++
Sbjct: 429 GAVPFVCIQLIMVALVIMFPEMV 451


Lambda     K      H
   0.331    0.148    0.443 

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: 712
Number of extensions: 36
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 445
Length of database: 503
Length adjustment: 33
Effective length of query: 412
Effective length of database: 470
Effective search space:   193640
Effective search space used:   193640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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:

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:

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:

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, or view the source code.

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