GapMind for catabolism of small carbon sources

 

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

Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_011383335.1 AMB_RS04550 C4-dicarboxylate ABC transporter permease

Query= uniprot:Q88NP0
         (426 letters)



>NCBI__GCF_000009985.1:WP_011383335.1
          Length = 427

 Score =  313 bits (802), Expect = 6e-90
 Identities = 152/423 (35%), Positives = 263/423 (62%), Gaps = 3/423 (0%)

Query: 1   MEAFILLGSFIVLILIGMPVAYALGLSALIGAW-WIDIPLQAMMIQVASGVNKFSLLAIP 59
           M + ++ G  IVL+L GMP++ +LGL+ L   + +  +P++++ +++ +G+ KF ++AIP
Sbjct: 1   MNSAVIFGLLIVLMLTGMPISISLGLTVLSFLFLFTQVPIESVALKLFTGIEKFEIMAIP 60

Query: 60  FFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGS 119
           FF+LAG  +  GG++RR++ FA  +VG   GGL L  +MA   F A+SGSS A   ++GS
Sbjct: 61  FFILAGNFLTHGGVARRMINFATAMVGHWYGGLGLAGVMACALFAAVSGSSPATVVAIGS 120

Query: 120 VLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPG 179
           +++P M ++G+P +F   V  +     +L PPS   V+Y++A     S+ +LFMAG++PG
Sbjct: 121 IILPAMVKQGFPNKFGAGVITTSGALGILIPPSLVMVMYAVAT--NTSVGALFMAGVIPG 178

Query: 180 LLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTAT 239
           L+L+ V+  +    A K +YP+       +  +   EA+WGL  +VI++GGI +GVFT T
Sbjct: 179 LVLATVLGAVTWYIAWKNDYPRLPPATWAQRFRAFREAIWGLALIVIVIGGIYTGVFTPT 238

Query: 240 ESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIP 299
           E+AA++ V++F + +F+Y+D   + + K++  +    ++++ +I  A  F +V+    IP
Sbjct: 239 EAAAMSAVYAFLIAVFVYKDMPLKGVGKILLSSASMSAMLLYIITNAVLFSFVLANENIP 298

Query: 300 SKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFG 359
             I    +         L+ +N +L++ G  M+ + ++LI+ PIL PV   +G+DP+HFG
Sbjct: 299 HAIADWIVGKELGVIAFLLVVNVLLLVAGNFMEPSSIVLIMAPILFPVAMKLGIDPIHFG 358

Query: 360 MIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419
           ++++VN+ +G+  PPVG  L+V S I K+ I     A+ P+ LA+   LM VTY P +S+
Sbjct: 359 ILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLAMLGFLMVVTYWPPLSI 418

Query: 420 WLP 422
           WLP
Sbjct: 419 WLP 421


Lambda     K      H
   0.329    0.142    0.418 

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: 586
Number of extensions: 40
Number of successful extensions: 4
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: 426
Length of database: 427
Length adjustment: 32
Effective length of query: 394
Effective length of database: 395
Effective search space:   155630
Effective search space used:   155630
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 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