GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfuromonas acetexigens DSM 1397

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092057792.1 BQ4888_RS13555 TRAP transporter large permease

Query= SwissProt::Q9HU16
         (427 letters)



>NCBI__GCF_900111775.1:WP_092057792.1
          Length = 431

 Score =  319 bits (817), Expect = 1e-91
 Identities = 168/419 (40%), Positives = 253/419 (60%), Gaps = 2/419 (0%)

Query: 5   FLFLLLFLLMFIG--VPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFF 62
           +L +L  LL  +   VP+ ++L  +G L +        R +   L+ + + + L+ + FF
Sbjct: 5   YLIILAVLLGALATTVPVFMALFFTGLLGLSWLMGIDPRIVIEVLYRSMDKFALIVVLFF 64

Query: 63  LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122
           +L G  MTTG +  +LI  AN  VG + GGLA+A +LAC LF A+SGS+ AT  A+G   
Sbjct: 65  VLCGNVMTTGTIVEKLIKTANVLVGCLPGGLAMAGILACGLFGAISGSTVATAVAIGGFM 124

Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182
           I  ++ +GY ++F  G++  A  LGI+IPPSI M++YA  T  S+  LF+ G +PG L+ 
Sbjct: 125 IPALIDNGYDESFSVGVMTTAPILGIVIPPSIAMILYAMVTNDSLEALFLTGFIPGALIM 184

Query: 183 LILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAA 242
           L + +  + V R K     PR +L E +A+ +++ W LLL  II  GIY G FT  EAA 
Sbjct: 185 LAMSIYAFFVCRAKGYAVRPRPTLAEAVATLKESFWALLLPAIIFIGIYGGIFTANEAAV 244

Query: 243 VAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIA 302
           VA  Y+ FV + ++RDMRL +  KV++ S   +  L+ I+A A +F   LT EQIP  IA
Sbjct: 245 VACFYAFFVEIVIHRDMRLRDVKKVIVASAITSATLLIIVAGASVFGEYLTFEQIPDKIA 304

Query: 303 SWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMV 362
           + V     SPW+FLL VNI+LL+ G FM+  +  LIL PIF P+  + G+D +H G++M 
Sbjct: 305 NGVVGNIQSPWVFLLAVNILLLVIGMFMDIISATLILTPIFLPLLAKFGVDTMHFGLLMT 364

Query: 363 VNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALP 421
           +N+ IG  TPP+G++L+++ A     L    RA  P+LMI ++ L++ T+ P + L LP
Sbjct: 365 INLGIGYCTPPLGVSLYISGATVNRDLLYVSRAVFPFLMIQILLLLLFTFWPDLVLLLP 423


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: 465
Number of extensions: 18
Number of successful extensions: 1
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: 431
Length adjustment: 32
Effective length of query: 395
Effective length of database: 399
Effective search space:   157605
Effective search space used:   157605
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