GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8502039 DvMF_2752 inner-membrane translocator (RefSeq)

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Miya:8502039
          Length = 330

 Score =  199 bits (505), Expect = 1e-55
 Identities = 132/335 (39%), Positives = 184/335 (54%), Gaps = 47/335 (14%)

Query: 12  AVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71
           AV + VLPL+L  +   W  +     LY +LAL LNI++G AGL  +G+ AFYAVGAY+ 
Sbjct: 13  AVVVAVLPLLLDPY---WTDVFVSIGLYSVLALSLNIILGQAGLFHMGHAAFYAVGAYVT 69

Query: 72  ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           A+      A+                LW  +P A L AA F  ++  P + LRGDYL IV
Sbjct: 70  AI------ANTMWGVPV---------LW-AMPFAGLAAALFAMVVARPIIHLRGDYLLIV 113

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYY 191
           T+G  EI+RI L N  +   LT G  G        +FG+    R  +FGF I     +YY
Sbjct: 114 TIGIVEIVRIALIN--NVFGLTGGANG--------IFGIS---RPMLFGFKIAKPVHFYY 160

Query: 192 LFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVS 251
           L    V  S+++  RL++SR GRA   I+ED+ AA+  G+N  + KL AF +GA + G++
Sbjct: 161 LVWAYVACSILLFRRLENSRFGRALNYIKEDDTAAEGSGVNIASYKLWAFVLGAFWAGMT 220

Query: 252 GAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311
           G ++ A    +SPESFS  ESV++ A+V+LGG G   GV+LGA LL  LPE  R      
Sbjct: 221 GTIYAAKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPEFFR------ 273

Query: 312 QAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
                   + A  R L   LAM+++M+ RP+G+ P
Sbjct: 274 --------EFASARMLAFGLAMVVMMIFRPQGMLP 300


Lambda     K      H
   0.328    0.144    0.430 

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: 300
Number of extensions: 16
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: 358
Length of database: 330
Length adjustment: 29
Effective length of query: 329
Effective length of database: 301
Effective search space:    99029
Effective search space used:    99029
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 (21.7 bits)
S2: 49 (23.5 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