GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fumD in Pseudomonas stutzeri RCH2

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate GFF3134 Psest_3193 hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region/hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region

Query= BRENDA::Q141Z6
         (520 letters)



>lcl|FitnessBrowser__psRCH2:GFF3134 Psest_3193 hydro-lyases, Fe-S
           type, tartrate/fumarate subfamily, alpha
           region/hydro-lyases, Fe-S type, tartrate/fumarate
           subfamily, beta region
          Length = 507

 Score =  766 bits (1977), Expect = 0.0
 Identities = 376/499 (75%), Positives = 432/499 (86%), Gaps = 1/499 (0%)

Query: 14  MTVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAE 73
           MTVIKQ+DLIQS+AD+LQ+ISYYHP+D+IQA+  AY  E+SPAA+D++AQIL NSRMCA 
Sbjct: 1   MTVIKQDDLIQSVADALQFISYYHPVDFIQAMHEAYLREESPAARDSMAQILINSRMCAT 60

Query: 74  GKRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEG 133
           G RPICQDTGIVTVFV+VGMDVRWDGATM + DMINEGVRR Y  P+NVLRASI++ P G
Sbjct: 61  GHRPICQDTGIVTVFVRVGMDVRWDGATMSLDDMINEGVRRAYNLPENVLRASILADPAG 120

Query: 134 GRKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTM 193
            RKNTKDNTPAVIHY IVPG+ V+V VAAKGGGSENKSK AMLNPSDSIVDW+LKTVPTM
Sbjct: 121 SRKNTKDNTPAVIHYSIVPGDKVEVDVAAKGGGSENKSKMAMLNPSDSIVDWVLKTVPTM 180

Query: 194 GAGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNA 253
           GAGWCPPGMLGIGIGGTAEKA VMAKE LMDPIDI ++ ARGP++ IEE+R+EL +KVN 
Sbjct: 181 GAGWCPPGMLGIGIGGTAEKAAVMAKEVLMDPIDIHELKARGPQNRIEEMRLELFDKVNQ 240

Query: 254 LGIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSL 313
           LGIGAQGLGGL TVLDVKIM  PTHAAS PV +IPNCAATRHAHF LDGSG A L  P L
Sbjct: 241 LGIGAQGLGGLTTVLDVKIMDYPTHAASLPVCMIPNCAATRHAHFVLDGSGPAELTPPPL 300

Query: 314 DAWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAK 373
           DA+P++ W+     ++RV+L+T+TPEEV +W PG+T+LL+GKMLTGRDAAHKR+ DML K
Sbjct: 301 DAYPEIVWEAG-PSARRVNLDTITPEEVQSWKPGETILLNGKMLTGRDAAHKRMVDMLNK 359

Query: 374 GEKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAER 433
           GE+LPVD   R IYYVGPVDPV DE VGPAGPTTATRMDKFT  +L  TGL+ MIGK+ER
Sbjct: 360 GEELPVDLKGRFIYYVGPVDPVGDEVVGPAGPTTATRMDKFTRQILESTGLLGMIGKSER 419

Query: 434 GPVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAV 493
           GP+AIEAI+ +KA YLMAVGGAAYLV++AI+ +KVLAF +LGMEAIYEF+VQDMPVTVAV
Sbjct: 420 GPIAIEAIKDNKAVYLMAVGGAAYLVAQAIKKSKVLAFAELGMEAIYEFEVQDMPVTVAV 479

Query: 494 DSNGTSVHQTGPKEWQARI 512
           D+NG SVH TGP  WQ +I
Sbjct: 480 DTNGESVHITGPAIWQKKI 498


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: 948
Number of extensions: 33
Number of successful extensions: 2
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: 507
Length adjustment: 35
Effective length of query: 485
Effective length of database: 472
Effective search space:   228920
Effective search space used:   228920
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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