GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Pseudomonas simiae WCS417

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate GFF5513 PS417_28215 pyruvate carboxylase subunit A

Query= BRENDA::Q9I299
         (655 letters)



>FitnessBrowser__WCS417:GFF5513
          Length = 471

 Score =  406 bits (1044), Expect = e-117
 Identities = 213/466 (45%), Positives = 298/466 (63%), Gaps = 3/466 (0%)

Query: 8   IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67
           I+++L+ANRGEIA R++R+   +GI SVAV+SD DRHA HV  AD A  +G A+P   YL
Sbjct: 2   IKKILIANRGEIAVRIVRACAEMGIRSVAVYSDADRHALHVKRADEAHSIG-AEPLAGYL 60

Query: 68  RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127
              +++  A+ +G  A+HPGYGFLSENA+ A  C E G+ F+GP A  I  MG K+ A+ 
Sbjct: 61  NPRKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFIGPSAEVIRRMGDKTEARR 120

Query: 128 LMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEAL 187
            M +AGVP+ PG  G   D+     E  RIGYPV+LKA +GGGG+G++      EL +A 
Sbjct: 121 SMIKAGVPVTPGTEGNVADIHEALTEGDRIGYPVMLKATSGGGGRGIRRCNSREELEQAF 180

Query: 188 SSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEE 247
                EA  AFG A + +EK ++ P+H+E Q+  D  G+ ++L ERDCSIQRR+QK++E 
Sbjct: 181 PRVISEATKAFGSAEVFLEKCIVNPKHIEAQILGDSFGNVVHLFERDCSIQRRNQKLIEI 240

Query: 248 APAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTE 307
           AP+P L  E R  +G+ +VRAA+A+GY  AGTVEFLL E G+ +FMEMNTR+QVEH +TE
Sbjct: 241 APSPQLTPEQRAYIGDLSVRAAKAVGYENAGTVEFLLAE-GEVYFMEMNTRVQVEHTITE 299

Query: 308 AITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREA 367
            ITG+D+V  QIR+A G  L + QE +   G A++ R+ AEDP+ +FLP+ G++  Y  A
Sbjct: 300 EITGIDIVREQIRIASGLPLSVKQEDIQHRGFALQFRINAEDPKNNFLPSFGKITRY-YA 358

Query: 368 AAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLA 427
             GPG R D+ +  G  + PFYD M  KL+ W  T EEA  R L  L +  + G++T  A
Sbjct: 359 PGGPGVRTDTAIYTGYTIPPFYDSMCLKLVVWALTWEEAMDRGLRALDDMRLQGVKTTAA 418

Query: 428 FLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEA 473
           + + IL +P F + + +T F+  H +    + +  PE    A A A
Sbjct: 419 YYQEILRNPEFRSGQFNTSFVESHPELTNYSIKRKPEELALAIAAA 464


Lambda     K      H
   0.319    0.135    0.397 

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: 704
Number of extensions: 37
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: 655
Length of database: 471
Length adjustment: 36
Effective length of query: 619
Effective length of database: 435
Effective search space:   269265
Effective search space used:   269265
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 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