GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Escherichia coli BW25113

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 1937061 b3578 predicted transporter (NCBI)

Query= SwissProt::Q9HU16
         (427 letters)



>FitnessBrowser__Keio:1937061
          Length = 425

 Score =  295 bits (756), Expect = 1e-84
 Identities = 153/424 (36%), Positives = 249/424 (58%)

Query: 1   MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60
           M +L     L   + IG+PIA +L L GA  +       V+ +A  L   ++ ++LLAIP
Sbjct: 1   MAVLIFLGCLLGGIAIGLPIAWALLLCGAALMFWLDMFDVQIMAQTLVNGADSFSLLAIP 60

Query: 61  FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120
           FF+L+G  M  GG+++R++D     VGH  GGL    VLA M+ A+LSGS+ A  AAV +
Sbjct: 61  FFVLAGEIMNAGGLSKRIVDLPMKLVGHKPGGLGYVGVLAAMIMASLSGSAVADTAAVAA 120

Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180
           + +  M  + YP    AG++ + G +  +IPPSI  +++  ++  S+ KLF+AG+ PG++
Sbjct: 121 LLVPMMRSANYPVNRAAGLIASGGIIAPIIPPSIPFIIFGVSSGLSISKLFMAGIAPGMM 180

Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240
           +G  LM+  +  A    LP   + +++E   S    +W L L VII+GG  SG FTPTEA
Sbjct: 181 MGATLMLTWWWQASRLNLPRQQKATMQEIWHSFVSGIWALFLPVIIIGGFRSGLFTPTEA 240

Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300
            AVAA Y+ FVA  +YR+M  +    VL+ + K T ++MF++A+A + A ++T  ++P  
Sbjct: 241 GAVAAFYALFVATVIYREMTFATLWHVLIGAAKTTSVVMFLVASAQVSAWLITIAELPMM 300

Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360
           ++  +  L  SP +  +V+ + +LI G  M+ +  +LIL P+  P+  E GIDPI+ G++
Sbjct: 301 VSDLLQPLVDSPRLLFIVIMVAILIVGMVMDLTPTVLILTPVLMPLVKEAGIDPIYFGVM 360

Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420
            ++N  IGLITPP+G  L V S V  +     +R   P++++L   L++  +IP + +  
Sbjct: 361 FIINCSIGLITPPIGNVLNVISGVAKLKFDDAVRGVFPYVLVLYSLLVVFVFIPDLIILP 420

Query: 421 PNWL 424
             W+
Sbjct: 421 LKWI 424


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: 14
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: 425
Length adjustment: 32
Effective length of query: 395
Effective length of database: 393
Effective search space:   155235
Effective search space used:   155235
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 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