GapMind for catabolism of small carbon sources

 

Aligments for a candidate for btsT in Cupriavidus basilensis 4G11

Align Pyruvate/proton symporter BtsT; Brenztraubensaure transporter; Pyruvate/H(+) symporter (characterized)
to candidate RR42_RS20515 RR42_RS20515 carbon starvation protein A

Query= SwissProt::P39396
         (716 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS20515 RR42_RS20515 carbon
           starvation protein A
          Length = 690

 Score =  902 bits (2332), Expect = 0.0
 Identities = 457/704 (64%), Positives = 553/704 (78%), Gaps = 25/704 (3%)

Query: 5   KIFKHIPWVILGIIGAFCLAVVALRRGEHISALWIVVASVSVYLVAYRYYSLYIAQKVMK 64
           +I +H+ W+ + I+GAF  A VAL RGE +SALWIVVA++ +YL+AYRYYS +IA+KVM+
Sbjct: 3   RIGQHLVWLAVAILGAFAFATVALSRGEAVSALWIVVAAICIYLIAYRYYSKFIAEKVMQ 62

Query: 65  LDPTRATPAVINNDGLNYVPTNRYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLLA 124
           LDP R TPA  +NDGL+YVPTN+ VLFGHHFAAIAGAGPLVGPVLAAQMGY+PG LW+LA
Sbjct: 63  LDPKRMTPAWRHNDGLDYVPTNKAVLFGHHFAAIAGAGPLVGPVLAAQMGYMPGMLWILA 122

Query: 125 GVVLAGAVQDFMVLFISSRRNGASLGEMIKEEMGPVPGTIALFGCFLIMIIILAVLALIV 184
           GVV AGAVQDFMVLFIS+RR+G SLG++IK EMG VPG IALFGCF+IMIIILAVLALIV
Sbjct: 123 GVVFAGAVQDFMVLFISTRRDGRSLGDLIKSEMGTVPGMIALFGCFMIMIIILAVLALIV 182

Query: 185 VKALAESPWGVFTVCSTVPIALFMGIYMRFIRPGRVGEVSVIGIVLLVASIYFGGVIAHD 244
           VKALA SPWG FTV  T+PIALFMGIY R+IRPGR+GEVSVIG VLL+ +I  G  +   
Sbjct: 183 VKALAGSPWGTFTVGVTIPIALFMGIYTRYIRPGRIGEVSVIGFVLLMLAIIGGQYVHES 242

Query: 245 PYWGPALTFKDTTITFALIGYAFVSALLPVWLILAPRDYLATFLKIGVIVGLALGIVVLN 304
               P  T+    +T+ LI Y F++A+LPVWL+LAPRDYL+TFLKIG I+ LA+GI+++ 
Sbjct: 243 AVLAPLFTYDGKALTWMLIIYGFIAAVLPVWLLLAPRDYLSTFLKIGTIIALAIGILIVA 302

Query: 305 PELKMPAMTQYIDGTGPLWKGALFPFLFITIACGAVSGFHALISSGTTPKLLANETDARF 364
           PELKMPA TQ+  G GP+W G LFPFLFITIACGAVSGFHALISSGTTPKLL +E   RF
Sbjct: 303 PELKMPAFTQFAKGGGPVWSGNLFPFLFITIACGAVSGFHALISSGTTPKLLESEAHMRF 362

Query: 365 IGYGAMLMESFVAIMALVAASIIEPGLYFAMNTPPAGLGITMPNLHEMGGENAPIIMAQL 424
           IGYGAML ESFVAIMALVAAS+IEPG+YFAMN+P A +G             +P  +AQ+
Sbjct: 363 IGYGAMLAESFVAIMALVAASVIEPGVYFAMNSPAAVIG------------TSPESVAQV 410

Query: 425 KDVTAHAAATVSSWGFVISPEQILQTAKDIGEPSVLNRAGGAPTLAVGIAHVFHKVL-PM 483
                     VS WGFVI+P+ ++QTAKD+GE S+++RAGGAPTLAVGIAH+ H+V+   
Sbjct: 411 ----------VSGWGFVITPDVLIQTAKDVGENSIISRAGGAPTLAVGIAHILHQVVGGQ 460

Query: 484 ADMGFWYHFGILFEALFILTALDAGTRSGRFMLQDLLGNFIPFLKKTDSLVAGIIGTAGC 543
           A M FWYHF ILFEALFILTA+DAGTR+GRFMLQDLLG+F+P  ++TDSL A +I TA  
Sbjct: 461 AMMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPSFRRTDSLPANLIATALT 520

Query: 544 VGLWGYLLYQGVVDPLGGVKSLWPLFGISNQMLAAVALVLGTVVLIKMKRTQYIWVTVVP 603
           V  WGY LYQGVVDPLGG+ +LWPLFGISNQMLAAVALVLGT VL+KMKR QY WVT+VP
Sbjct: 521 VSFWGYFLYQGVVDPLGGINTLWPLFGISNQMLAAVALVLGTCVLVKMKRGQYAWVTLVP 580

Query: 604 AVWLLICTTWALGLKLFSTNPQMEGFFYMASQYKEKIANGTDLT-AQQIANMNHIVVNNY 662
            +WLLICT  A   KLF  +P++  F   A+++ + IA G  L  A+ +  M+ IV N+Y
Sbjct: 581 TIWLLICTLTAGWQKLFDADPKV-SFLTHAAKFSDAIAQGKVLAPAKSMEQMHRIVFNDY 639

Query: 663 TNAGLSILFLIVVYSIIFYGFKTWLAVRNSDKRTDKETPYVPIP 706
            +AGL  LF+ VV SI+FYGFKT +  R  ++ TD+ETP+ P+P
Sbjct: 640 LDAGLCALFMFVVLSIVFYGFKTAMKARAENRPTDRETPFEPMP 683


Lambda     K      H
   0.327    0.142    0.440 

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: 1446
Number of extensions: 73
Number of successful extensions: 7
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: 716
Length of database: 690
Length adjustment: 39
Effective length of query: 677
Effective length of database: 651
Effective search space:   440727
Effective search space used:   440727
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: 54 (25.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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