GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Magnetospirillum magneticum AMB-1

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 WP_011384964.1 AMB_RS13000 C4-dicarboxylate ABC transporter

Query= TCDB::Q8YSQ7
         (445 letters)



>NCBI__GCF_000009985.1:WP_011384964.1
          Length = 486

 Score =  503 bits (1296), Expect = e-147
 Identities = 247/444 (55%), Positives = 333/444 (75%), Gaps = 13/444 (2%)

Query: 8   LGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYT 67
           + P+MFA  +  L  GYPVAF+L    I+FGL+GI LG+ +     A+P+RIFGIM N T
Sbjct: 9   MAPLMFAALVFFLLIGYPVAFALAANGIVFGLVGIELGLLNASLFQALPERIFGIMRNDT 68

Query: 68  LLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATV 127
           LLAIP+F FMG +LE+SG+AE LL+T+G L G +RGGLA AV+ VGALLAATTGVVAA+V
Sbjct: 69  LLAIPFFTFMGLILERSGMAEDLLDTIGQLFGPIRGGLAYAVIFVGALLAATTGVVAASV 128

Query: 128 VAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSV 187
           ++MGLISLPIMLRYGY++ +A+GVIAASGTL QIIPPS+VL+++ DQLG SVGD++ G+ 
Sbjct: 129 ISMGLISLPIMLRYGYDRRVASGVIAASGTLAQIIPPSLVLIIMADQLGRSVGDMYAGAF 188

Query: 188 IPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLG 247
           IPG ++   +A  + +V  IRP  APALP + R + G  L  R +  ++PPLILI LVLG
Sbjct: 189 IPGFVLTGLYAGFIFLVTMIRPSFAPALPPEARSLRGMGLLLRTVTCLVPPLILIFLVLG 248

Query: 248 SIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFS 307
           +IF G ATPTE GA+G AGA+ LA    +     +RQ  DTT +++  VVFIL+GST F 
Sbjct: 249 TIFIGVATPTEGGAMGAAGAMILALMKRKLDWNLMRQAMDTTAKLSCFVVFILVGSTVFG 308

Query: 308 LVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQK 367
           LVFRG+NGD ++  ++++LPGGK+GFL V+   +F+L FF+DFFE+AFI++PL  PVA+K
Sbjct: 309 LVFRGVNGDLWVEHLMSSLPGGKLGFLIVTNVLMFVLAFFLDFFELAFILVPLLGPVAEK 368

Query: 368 LGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAP-------------PEVTTSDIYR 414
           +GIDL+W+GV+LG N+QTSF+ PPFGFALFYLR VAP             P++TT  IY 
Sbjct: 369 MGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAPKTDYIDKITNKLTPKITTGQIYW 428

Query: 415 GVIPFILLQLLVLLLIIIFPGIVS 438
           G +PF+++Q++++ L+I FP +V+
Sbjct: 429 GAVPFVIIQIIMVGLVIAFPDLVT 452


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: 692
Number of extensions: 28
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: 486
Length adjustment: 33
Effective length of query: 412
Effective length of database: 453
Effective search space:   186636
Effective search space used:   186636
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