GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfovibrio vulgaris Hildenborough

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 208936 DVU0009 DedA family protein

Query= SwissProt::Q9HU16
         (427 letters)



>MicrobesOnline__882:208936
          Length = 426

 Score =  313 bits (801), Expect = 8e-90
 Identities = 171/414 (41%), Positives = 251/414 (60%), Gaps = 1/414 (0%)

Query: 1   MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60
           MT L LF +L LL     PI +++G S    +L+           +L+  ++ + LLA+P
Sbjct: 1   MTALVLFGMLGLLFACNAPIMLAVGASAFAALLIKGGMDPMVAVQRLYAGADSFPLLAVP 60

Query: 61  FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120
            F+ +G  M+ GG+++R++  A+  VGH+ GGLA+ +V++ M FA +SGS+ A  AAVGS
Sbjct: 61  LFMTAGQLMSAGGISQRIVRLADTLVGHLPGGLAVVSVVSSMFFAGVSGSAAADTAAVGS 120

Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180
           I I  MV  GY  AF   +   AG++G++IPPSI M+V+ A T  S+GKLF  GV+PGLL
Sbjct: 121 ILIPSMVARGYSPAFAGAVQAAAGSIGVVIPPSIPMIVFGALTGASIGKLFAGGVMPGLL 180

Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240
           +G+ L                       W A  R A W L    IILGGI SG  T TEA
Sbjct: 181 MGITLSAWCVHEGLRSGRETRRFEPAAVWPALLR-AGWSLGAPAIILGGIISGVCTATEA 239

Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300
           AAVA VY+  V LF +R++ L   P +LL++   + ++M IIA A LF  V+  E+IP +
Sbjct: 240 AAVAVVYAFLVGLFAHRELDLRRLPALLLDAAVTSGVVMSIIAAASLFGWVMAIERIPAA 299

Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360
           +A  +  +G   WM LL VNI+LL+AG  +E +A +++L P+   +   +GID IHLG+I
Sbjct: 300 LADAILAVGGEGWMLLLAVNILLLLAGTMLETTAALILLVPVLVQLLPRMGIDLIHLGVI 359

Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIP 414
           +V+N+ IG++TPP+G+ L V+  +  +PL    RA LP L +L+V L++VTYIP
Sbjct: 360 VVMNLSIGMLTPPLGVCLMVSCGIARVPLATLARAVLPLLAVLVVDLMLVTYIP 413


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: 508
Number of extensions: 31
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: 427
Length of database: 426
Length adjustment: 32
Effective length of query: 395
Effective length of database: 394
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 (21.9 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