GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ectP in Dietzia timorensis ID05-A0528

Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate WP_082908457.1 BJL86_RS11120 BCCT family transporter

Query= SwissProt::Q87PP5
         (562 letters)



>NCBI__GCF_001659785.1:WP_082908457.1
          Length = 597

 Score =  318 bits (815), Expect = 4e-91
 Identities = 181/474 (38%), Positives = 281/474 (59%), Gaps = 36/474 (7%)

Query: 108 DAFFMWSTN-----FFLL------FAVGLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAA 156
           D+ F W+T      F L+      F + L  S  G IR+G     P++ T SW++M+FAA
Sbjct: 78  DSAFSWTTGNLGWAFVLIQTSAVGFVIYLALSKYGAIRIGADGERPEYRTGSWIAMMFAA 137

Query: 157 GMGIGLLFWSVAEPTAYFTDWWGTPLNAEAYSADAKSLAMGATMFHWGVHGWSIYALVAL 216
           GMGIGL+F+ V+EP A+F D                 +A+  T FHWG+H WS YA+V L
Sbjct: 138 GMGIGLMFFGVSEPLAHFHD------APPGVDEPTYGMALATTAFHWGMHPWSGYAVVGL 191

Query: 217 ALAFFAFNKGLPLSLRAAFYPIFGDR-AWGWLGHVIDILAVLSTLFGLATSLGLGAQQAT 275
           ALA  A+  G    +  A  P+ G++ A G LG  +D+L +L+T+FG A SLGLGA Q  
Sbjct: 192 ALALTAYRYGRTHLISQAMIPVIGEKNAKGGLGKFLDVLTILATIFGTACSLGLGALQIQ 251

Query: 276 SGINHVFGLNG-GIGTQMVVIAFVTFIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITF 334
           +G+N    ++  GIG  + VI  +    ++S   G+  G++LLSN+NM++A  L +F+  
Sbjct: 252 TGLNETGAISTTGIGIVIGVIVVLGLAFLVSAASGVSKGIQLLSNINMVLALCLALFVAI 311

Query: 335 ITFDTAMG-SLVDTTMA-YIQNIIPLSNPHGR----EDETWMHGWTVFYWAWWVSWSPFV 388
            +    +  +L+ T++  Y+QN + +++  G     E   W+  WT+FYWAWWVSWSPFV
Sbjct: 312 FSGALVLILNLIPTSLGQYLQNFLDMASRTGASQNGEAGEWLGSWTIFYWAWWVSWSPFV 371

Query: 389 GMFIARVSKGRTVREFLFAVIVIPTLVTLVWMSVFGGIALDQVVNKVGELGANGLTDISL 448
           GMF+AR+S+GRT+R+F+  V+++P  +++VW S+FGG AL   +  +G+     + D  +
Sbjct: 372 GMFLARISRGRTIRQFVAGVVLVPAGMSIVWFSIFGGTALH--LEAIGDT----IRDAEV 425

Query: 449 T---LFHVYDVLPYSSVISILSIVLILVFFITSSDSGSLVIDSITAGGKIDAPVPQRIFW 505
           +   LF+V   LP S++I IL++ LI +FFITS+DS S+V+  +   G  +      +F+
Sbjct: 426 SERELFNVASNLPGSTIIMILAMALIAIFFITSADSASVVMGGMGQYGIEEPARYVTVFF 485

Query: 506 ACIEGSIAAVMLWV--GGKEALQALQSGVVATGLPFTFVLLLMCVSLVKGLRTE 557
               G+IA +ML    GG EAL +LQS  +    PF  +L+++ VS++K LR +
Sbjct: 486 GICTGAIAIIMLLAGGGGSEALDSLQSITIIAASPFLIILVVLAVSIMKMLRAD 539


Lambda     K      H
   0.327    0.141    0.445 

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: 913
Number of extensions: 50
Number of successful extensions: 8
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: 562
Length of database: 597
Length adjustment: 36
Effective length of query: 526
Effective length of database: 561
Effective search space:   295086
Effective search space used:   295086
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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