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_011383335.1 AMB_RS04550 C4-dicarboxylate ABC transporter permease

Query= TCDB::Q8YSQ7
         (445 letters)



>NCBI__GCF_000009985.1:WP_011383335.1
          Length = 427

 Score =  207 bits (528), Expect = 4e-58
 Identities = 135/434 (31%), Positives = 226/434 (52%), Gaps = 20/434 (4%)

Query: 11  VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70
           V+F   +VL+ +G P++ SLG   + F      L +F  + + ++  ++F  +  + ++A
Sbjct: 5   VIFGLLIVLMLTGMPISISLGLTVLSF------LFLFTQVPIESVALKLFTGIEKFEIMA 58

Query: 71  IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130
           IP+FI  G  L   G+A R++     ++G   GGL LA V+  AL AA +G   ATVVA+
Sbjct: 59  IPFFILAGNFLTHGGVARRMINFATAMVGHWYGGLGLAGVMACALFAAVSGSSPATVVAI 118

Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190
           G I LP M++ G+  +   GVI  SG LG +IPPS+V+V+       SVG LF+  VIPG
Sbjct: 119 GSIILPAMVKQGFPNKFGAGVITTSGALGILIPPSLVMVMYAVATNTSVGALFMAGVIPG 178

Query: 191 LMMASAFALHVLIVAFIR--PDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGS 248
           L++A+        +A+    P + PA  AQ           R  +  I  L LI++V+G 
Sbjct: 179 LVLATVLGAVTWYIAWKNDYPRLPPATWAQ---------RFRAFREAIWGLALIVIVIGG 229

Query: 249 IFFGFATPTEAGAVGCAGAIALAA-ANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFS 307
           I+ G  TPTEA A+    A  +A        L+ + ++  ++  +++M+++I+  +  FS
Sbjct: 230 IYTGVFTPTEAAAMSAVYAFLIAVFVYKDMPLKGVGKILLSSASMSAMLLYIITNAVLFS 289

Query: 308 LVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQK 367
            V    N    + D +     G I FL V    + + G F++   I  I+ P+  PVA K
Sbjct: 290 FVLANENIPHAIADWIVGKELGVIAFLLVVNVLLLVAGNFMEPSSIVLIMAPILFPVAMK 349

Query: 368 LGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVL 427
           LGID + +G+++  N++     PP G  L+   G+    +T  ++   V P++L  L  L
Sbjct: 350 LGIDPIHFGILIVVNMEVGMCHPPVGLNLYVASGITKMGIT--ELTVAVWPWLLAMLGFL 407

Query: 428 LLIIIFPGIVSFLP 441
           +++  +P +  +LP
Sbjct: 408 MVVTYWPPLSIWLP 421


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: 442
Number of extensions: 19
Number of successful extensions: 3
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: 427
Length adjustment: 32
Effective length of query: 413
Effective length of database: 395
Effective search space:   163135
Effective search space used:   163135
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.

Links

Downloads

Related tools

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