GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Halomonas desiderata SP1

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_086510167.1 BZY95_RS12010 TRAP transporter large permease

Query= SwissProt::Q9HU16
         (427 letters)



>NCBI__GCF_002151265.1:WP_086510167.1
          Length = 423

 Score =  351 bits (901), Expect = e-101
 Identities = 182/419 (43%), Positives = 272/419 (64%)

Query: 4   LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFL 63
           L LFLLL +L  IGVPIA SLGL+ A+T+       +  +A +   +   + L+AIPFF+
Sbjct: 3   LLLFLLLIVLFVIGVPIAFSLGLASAITVWQGELMPMLIVAQQYITSVNSFPLMAIPFFI 62

Query: 64  LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123
           L+G  M +GG++RRL+DF+N  VG + GGLA+ A++  + FAA+SGS  AT AA+G+I I
Sbjct: 63  LAGYLMQSGGISRRLVDFSNTIVGSMTGGLAMVAIVTSLFFAAISGSGAATTAAIGAILI 122

Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGL 183
             M+  GY   + A     +G LG++IPPSI +++Y  A   SVG +F+AG++PGL++ L
Sbjct: 123 PAMIAKGYASGYAAANQAASGALGVIIPPSIPLILYGIAANVSVGDMFVAGILPGLMITL 182

Query: 184 ILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAAV 243
            L++  Y  AR        R S RE   + RKAL  +L+ VIILGGIY G FTPTEAA +
Sbjct: 183 SLLLFAYGYARYHGHGGGERSSWREMFTAGRKALLAILMPVIILGGIYGGIFTPTEAAVI 242

Query: 244 AAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIAS 303
           A VYS  V   +YR++ L +   +L E+   T +++ II  A L+  +L + ++P  +++
Sbjct: 243 AVVYSFLVGFVIYREISLKDIVGILQEAAVTTAVVLSIIGAAGLYGRILQSLRVPSMLSN 302

Query: 304 WVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVV 363
           +V     SP +F+++VN++LL+AG F+E +A ILI  PI  PIA+  G DP+H GIIMVV
Sbjct: 303 FVIGAIDSPLLFIVLVNVLLLMAGMFIEAAAAILIFVPILLPIAVSFGFDPVHFGIIMVV 362

Query: 364 NMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALPN 422
           N+ +G+ TPPVGLNLFV S ++ + +     + LP++ I+LV L I++ +P +S  LP+
Sbjct: 363 NLAMGMFTPPVGLNLFVASQISKVGVARLTWSILPFVAIVLVNLFIISVVPFLSTWLPS 421


Lambda     K      H
   0.330    0.144    0.425 

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: 487
Number of extensions: 15
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: 427
Length of database: 423
Length adjustment: 32
Effective length of query: 395
Effective length of database: 391
Effective search space:   154445
Effective search space used:   154445
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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