GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Azospirillum brasilense Sp245

Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate AZOBR_RS20015 AZOBR_RS20015 C4-dicarboxylate ABC transporter

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__azobra:AZOBR_RS20015
          Length = 503

 Score =  514 bits (1323), Expect = e-150
 Identities = 253/445 (56%), Positives = 338/445 (75%), Gaps = 13/445 (2%)

Query: 6   EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMAN 65
           E + P+MFA  ++ L  G+PVAF+L    +LFGL+GI LG+  P    A+P+R+FGIM N
Sbjct: 7   ENMAPLMFAALVLFLLMGFPVAFALAANGLLFGLIGIELGLLTPALFQALPERVFGIMRN 66

Query: 66  YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125
            TLLAIP+F FMG +LE+SG+AE LL+T+G L G LRGGLA AV+ VGALLAATTGVVAA
Sbjct: 67  DTLLAIPFFTFMGLILERSGMAEDLLDTVGQLFGPLRGGLAYAVIFVGALLAATTGVVAA 126

Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIG 185
           +V++MGLISLPIMLRYGY++ LA+GVIAASGTL QIIPPS+VL++L DQLG SVGD++ G
Sbjct: 127 SVISMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIILADQLGRSVGDMYAG 186

Query: 186 SVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLV 245
           +++PGL++   +A ++L+V+ +RP+  PALP + R + G  L  RV+  ++PPL+LI LV
Sbjct: 187 ALVPGLVLTGLYAGYILVVSIVRPEFTPALPPEARSLRGFQLLFRVLTSLVPPLVLIFLV 246

Query: 246 LGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTA 305
           LG+IF G ATPTE GA+G AGA+ LA    Q +   +RQ  DTT +++S V+FILIGST 
Sbjct: 247 LGTIFIGIATPTEGGAMGAAGAMILALMKRQLSWSLMRQAMDTTAKLSSFVIFILIGSTV 306

Query: 306 FSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVA 365
           F LVFR +NGD ++  +L +LPGG++GFL V    VFLL FF+DFFE+AFI++PL  PVA
Sbjct: 307 FGLVFRAVNGDLWVEHLLTSLPGGELGFLIVVNIMVFLLAFFLDFFELAFIIVPLLAPVA 366

Query: 366 QKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPE-------------VTTSDI 412
           +KLGIDL+W+GV+LG N+QTSF+ PPFGFALF+LR VAP E             +TT  I
Sbjct: 367 EKLGIDLIWFGVLLGVNMQTSFMHPPFGFALFFLRSVAPREDYKDKITGKIIKKITTGQI 426

Query: 413 YRGVIPFILLQLLVLLLIIIFPGIV 437
           Y G +PF+ +QL+++ L+I+FP +V
Sbjct: 427 YWGAVPFVCIQLIMVALVIMFPEMV 451


Lambda     K      H
   0.331    0.149    0.437 

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: 721
Number of extensions: 29
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:

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