Alignments for a candidate for fumD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fumD in Klebsiella michiganensis M5al

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate BWI76_RS08450 BWI76_RS08450 fumarate hydratase

Query= BRENDA::P0AC33
         (548 letters)



>FitnessBrowser__Koxy:BWI76_RS08450
          Length = 550

 Score =  768 bits (1983), Expect = 0.0
 Identities = 367/545 (67%), Positives = 441/545 (80%), Gaps = 1/545 (0%)

Query: 3   NKPFHYQAPFPLKKDDTEYYLLTSEHVSVSEFEGQEILKVAPEALTLLARQAFHDASFML 62
           +KPF +Q  F    D+TEY LLT++HV V+E +G+E++KVAPEALTLLA+QAF++ASF L
Sbjct: 2   SKPFVWQELFVQSNDNTEYELLTNQHVKVTELDGEEVIKVAPEALTLLAQQAFYEASFFL 61

Query: 63  RPAHQQQVADILRDPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAIIVGKKGQRVW 122
           R  H +Q+A IL DP+AS NDKYVALQ LRN++++AKGVLP CQDTGTA IV  KGQ VW
Sbjct: 62  RAGHLKQIASILHDPQASSNDKYVALQLLRNAEVSAKGVLPNCQDTGTATIVASKGQNVW 121

Query: 123 TGGGDEAALARGVYNTYIEDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYAVDGDEYKFLC 182
           TGG D  AL++G+Y T+ E+NLRYSQNAPLDMY EVNT TNLPAQID+ A  G EY+FL 
Sbjct: 122 TGGNDAEALSQGIYTTFQENNLRYSQNAPLDMYTEVNTQTNLPAQIDISAAPGSEYRFLF 181

Query: 183 IAKGGGSANKTYLYQETKALLTPGKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAETNL 242
           + KGGGSANK  L+QETK++L P KL  +L EKM+ LGTAACPPYHIAFV+GG SA+  L
Sbjct: 182 VNKGGGSANKAALFQETKSILQPEKLTAFLTEKMKALGTAACPPYHIAFVVGGLSADQAL 241

Query: 243 KTVKLASAKYYDELPTEGNEHGQAFRDVELEKELLIEAQNLGLGAQFGGKYFAHDIRVIR 302
           K  KLAS KYYD LPT GNE GQAFRD  LE  LL  ++  G+GAQFGGKYFAHDIRVIR
Sbjct: 242 KVAKLASTKYYDNLPTSGNELGQAFRDTSLEAALLKASREFGIGAQFGGKYFAHDIRVIR 301

Query: 303 LPRHGASCPVGMGVSCSADRNIKAKINRQGIWIEKLEHNPGKYIPEELRKAGEGEAVRVD 362
           LPRHG SCP+ M +SCSADRNIKAKIN+ GIW+EKLEHNPGK+IP+  R     ++V++D
Sbjct: 302 LPRHGGSCPIAMALSCSADRNIKAKINKHGIWLEKLEHNPGKFIPDSQRIENGAQSVQLD 361

Query: 363 LNRPMKEILAQLSQYPVSTRLSLNGTIIVGRDIAHAKLKERMDNGEGLPQYIKDHPIYYA 422
           LNRP++EIL ++S  PV TRLSL+G I+V RDIAHAKLKER+DNGE +P+Y+++H +YYA
Sbjct: 362 LNRPLREILREMSTLPVGTRLSLSGPIVVARDIAHAKLKERLDNGEPMPEYMRNHIVYYA 421

Query: 423 GPAKTPEGYASGSLGPTTAGRMDSYVDQLQAQGGSMIMLAKGNRSQQVTDACKKHGGFYL 482
           GPAKTP   A GSLGPTT GRMD YVD  QA GGS+IML+KGNRSQQVTDAC KHGGF L
Sbjct: 422 GPAKTPNNLACGSLGPTTGGRMDGYVDAFQAAGGSLIMLSKGNRSQQVTDACHKHGGFNL 481

Query: 483 GSIGGPAAVLAQGSIKSLECVEYPELGMEAIWKIEVEDFPAFILVDDKGNDFFQQIQ-LT 541
           GSIGG AA+LAQ  +KSL C+EYPELGMEA+W +EV++ PAF+LVDDKGN+FF Q +   
Sbjct: 482 GSIGGAAALLAQQYVKSLRCLEYPELGMEAVWMMEVDNLPAFVLVDDKGNNFFSQFEHQH 541

Query: 542 QCTRC 546
           +C  C
Sbjct: 542 RCATC 546


Lambda     K      H
   0.317    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: 1025
Number of extensions: 28
Number of successful extensions: 1
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: 548
Length of database: 550
Length adjustment: 36
Effective length of query: 512
Effective length of database: 514
Effective search space:   263168
Effective search space used:   263168
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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