Alignments for a candidate for fumD in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for fumD in Dinoroseobacter shibae DFL-12

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate 3608019 Dshi_1426 hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit (RefSeq)

Query= BRENDA::Q141Z6
         (520 letters)



>FitnessBrowser__Dino:3608019
          Length = 504

 Score =  602 bits (1551), Expect = e-176
 Identities = 295/495 (59%), Positives = 384/495 (77%), Gaps = 3/495 (0%)

Query: 15  TVIKQEDLIQSIADSLQYISYYHPLDYIQALGRAYELEQSPAAKDAIAQILTNSRMCAEG 74
           TV+K +D+++++  +LQYI+ YH  DY+  L  AY  EQSPAAK A+ QIL +SR+ A G
Sbjct: 5   TVLKPDDIVETVRAALQYIAVYHAPDYLAHLASAYAREQSPAAKAAMGQILESSRLAALG 64

Query: 75  KRPICQDTGIVTVFVKVGMDVRWDGATMGVTDMINEGVRRGYLNPDNVLRASIVSPPEGG 134
           +RPICQDTG+VTVF ++G      G    + +++NEGVR  YL+  N LRAS+V+ P   
Sbjct: 65  RRPICQDTGMVTVFARLGQSAMIAGDRT-LYELVNEGVRLAYLDAGNPLRASMVADPLLE 123

Query: 135 RKNTKDNTPAVIHYEIVPGNTVDVQVAAKGGGSENKSKFAMLNPSDSIVDWILKTVPTMG 194
           R+NT DNTPAV H E+  GN +++ +AAKGGGSENK+++ MLNP+ S+ DW++ T+  +G
Sbjct: 124 RRNTGDNTPAVTHVELTRGNKLELLIAAKGGGSENKARYTMLNPAASVEDWVVSTIEGLG 183

Query: 195 AGWCPPGMLGIGIGGTAEKAMVMAKESLMDPIDIQDVIARGPKDWIEELRVELHEKVNAL 254
           AGWCPPG++G+G+GG+AE+AM++AK ++M+ ID+ D++ARG    +EE+RV L+ ++NAL
Sbjct: 184 AGWCPPGLVGVGVGGSAEQAMLIAKRAVMEEIDMSDLLARGASTPLEEMRVRLYHRINAL 243

Query: 255 GIGAQGLGGLATVLDVKIMAAPTHAASKPVAIIPNCAATRHAHFTLDGSGAARLEAPSLD 314
           GIGAQGLGGL TV+DVK+  APTHAASKPVA++P CAA RHA   +DGSG A L+AP L 
Sbjct: 244 GIGAQGLGGLTTVVDVKLATAPTHAASKPVALVPQCAANRHAKVVMDGSGPAYLDAPDLA 303

Query: 315 AWPKVHWQPDTEKSKRVDLNTLTPEEVAAWTPGQTLLLSGKMLTGRDAAHKRIADMLAKG 374
           AWP++    +    +RV+++ LT EE+A W PG+TLLLSG++LTGRDAAHKR+ADMLA+G
Sbjct: 304 AWPRIEGS-EMAGLRRVNVDRLTREEMAGWAPGETLLLSGRILTGRDAAHKRMADMLARG 362

Query: 375 EKLPVDFTNRVIYYVGPVDPVRDEAVGPAGPTTATRMDKFTEMMLAQTGLISMIGKAERG 434
           E+LPV    RVIYYVGPVDPV  EAVGPAGPTTATRMD FT  ML Q GL +MIGKAERG
Sbjct: 363 EELPVSLRGRVIYYVGPVDPVDGEAVGPAGPTTATRMDPFTSDMLGQ-GLFAMIGKAERG 421

Query: 435 PVAIEAIRKHKAAYLMAVGGAAYLVSKAIRSAKVLAFEDLGMEAIYEFDVQDMPVTVAVD 494
              +  I +HKAAYL+AVGGAA LV+KAIRS+KVLAFEDLGMEAI EF V+DMPV VAV 
Sbjct: 422 AETVRDIARHKAAYLIAVGGAAVLVAKAIRSSKVLAFEDLGMEAIREFTVEDMPVMVAVT 481

Query: 495 SNGTSVHQTGPKEWQ 509
           + G ++HQTGP  W+
Sbjct: 482 TQGAAIHQTGPAAWR 496


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: 783
Number of extensions: 24
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: 520
Length of database: 504
Length adjustment: 35
Effective length of query: 485
Effective length of database: 469
Effective search space:   227465
Effective search space used:   227465
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources