GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fumD in Shewanella oneidensis MR-1

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate 201373 SO2222 fumarate hydratase, class I, anaerobic, putative (NCBI ptt file)

Query= BRENDA::Q141Z6
         (520 letters)



>FitnessBrowser__MR1:201373
          Length = 516

 Score =  702 bits (1813), Expect = 0.0
 Identities = 342/499 (68%), Positives = 409/499 (81%), Gaps = 3/499 (0%)

Query: 16  VIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAEGK 75
           VIKQ D I+S+AD+LQYISYYHP D++ A+  AYE EQS AAKDAIAQIL NSRM AEGK
Sbjct: 12  VIKQADFIESVADALQYISYYHPKDFVDAMSEAYEREQSAAAKDAIAQILINSRMSAEGK 71

Query: 76  RPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEGGR 135
           RP+CQDTGIVT FVKVGM V+WD   M +  M++EGVRR Y NPDN LRASIV+ P G R
Sbjct: 72  RPLCQDTGIVTTFVKVGMGVKWDKTDMTIQQMVDEGVRRAYTNPDNPLRASIVADPAGSR 131

Query: 136 KNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTMGA 195
           KNTKDNTP+V+H ++VPGN V+V +AAKGGGSENK+K  MLNPSD I  W+ KT+PTMGA
Sbjct: 132 KNTKDNTPSVVHIDMVPGNHVEVAIAAKGGGSENKAKMVMLNPSDDIAAWVEKTLPTMGA 191

Query: 196 GWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNALG 255
           GWCPPGMLGIGIGGTAEKA V+AKE+LM+ +DI +++ARG +   E+LR+++ E+ N LG
Sbjct: 192 GWCPPGMLGIGIGGTAEKAAVLAKEALMESVDIHELMARGAQTTEEKLRLDIFERANNLG 251

Query: 256 IGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSLDA 315
           IGAQGLGGL TVLDVKI +APTHAASKPV +IPNCAATRH HF LDG+G A L  PSL  
Sbjct: 252 IGAQGLGGLTTVLDVKIKSAPTHAASKPVVMIPNCAATRHVHFHLDGTGPADLAPPSLSD 311

Query: 316 WPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKGE 375
           WP++  +  ++  +RV+L+T+T  ++  W  G+TLLLSGKMLTGRDAAHKRI  ++  GE
Sbjct: 312 WPEITREVGSD-VRRVNLDTVTQADIEQWQSGETLLLSGKMLTGRDAAHKRIQSLIESGE 370

Query: 376 KLP--VDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433
            LP  VDFT + IYYVGPVDPV +E VGPAGPTTATRMDKFT++ML +TGL+ MIGKAER
Sbjct: 371 GLPEGVDFTGKFIYYVGPVDPVGNEVVGPAGPTTATRMDKFTDLMLDKTGLMGMIGKAER 430

Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493
           GP  +E+I+KHKA YLMAVGGAAYLVSKAI+ ++V+AF DLGMEAIYEFDVQDMPVTVAV
Sbjct: 431 GPATVESIKKHKAVYLMAVGGAAYLVSKAIKKSRVVAFADLGMEAIYEFDVQDMPVTVAV 490

Query: 494 DSNGTSVHQTGPKEWQARI 512
           DSNG + H+TGP  W+  I
Sbjct: 491 DSNGVNAHETGPAIWKVNI 509


Lambda     K      H
   0.316    0.133    0.392 

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: 870
Number of extensions: 24
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: 520
Length of database: 516
Length adjustment: 35
Effective length of query: 485
Effective length of database: 481
Effective search space:   233285
Effective search space used:   233285
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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