Alignments for a candidate for paaZ1 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ1 in Herbaspirillum seropedicae SmR1

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate HSERO_RS20590 HSERO_RS20590 enoyl-CoA hydratase

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__HerbieS:HSERO_RS20590
          Length = 686

 Score =  771 bits (1990), Expect = 0.0
 Identities = 401/679 (59%), Positives = 486/679 (71%), Gaps = 10/679 (1%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L SF++G W  G+  S+ +H A++G A+     E +D   A + A + G PAL A+ F +
Sbjct: 8   LQSFIAGRWL-GQRPSQALHSAVNGSAVASTHEESIDFGEALEHARKTGLPALMALDFQQ 66

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123
           RAA+LKA+AK+L+  KE  YA+SA TGATRADSW+DIEGG GTLFTYAS+G+ E P   L
Sbjct: 67  RAAILKALAKYLMEHKEVLYAVSAHTGATRADSWIDIEGGSGTLFTYASIGANEFPSSNL 126

Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183
             E   + L K+G FA  H+L  + GVAVHINAFNFP WGMLEK APT+L GMP I+KPA
Sbjct: 127 VHEGPAMRLGKQGRFAGTHILVPRGGVAVHINAFNFPVWGMLEKFAPTFLAGMPCIVKPA 186

Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243
           TAT+ L +A V+ I  SGL+PEG++ L+ GS GDLL+ L +QDVVTFTGSA T   LR  
Sbjct: 187 TATSYLAEAAVRLIQQSGLLPEGSLQLVIGSTGDLLERLQAQDVVTFTGSADTAAKLRAH 246

Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303
           PN++A SIPF  EADSLNC +LG D+T D  EF LF++EV REMTTKAGQKCTAIRR IV
Sbjct: 247 PNLIANSIPFNAEADSLNCAILGPDITADDEEFDLFVKEVAREMTTKAGQKCTAIRRAIV 306

Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKV-------NILLAA 356
           P+  V+AV++ L ARL K+VVGDPA E V+MG L +  Q+ DV+E+V       +++L A
Sbjct: 307 PRRHVDAVAERLAARLSKIVVGDPALETVRMGPLASRAQQRDVEERVALLRHSADLILGA 366

Query: 357 GCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLA 416
           G      GQ      GAFF PTLL          VH  EAFGPV+TLMP  +   AL LA
Sbjct: 367 GSAFAPQGQG--VGEGAFFAPTLLLARDTAAGSPVHEVEAFGPVSTLMPYDDLDEALALA 424

Query: 417 CAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPG 476
             G GSL  +LVT  P +A + I  AA  HGR+ +L+ E+A ESTGHGSPLPQL HGGPG
Sbjct: 425 ARGRGSLVASLVTRTPAVAARAIPVAAAWHGRLLVLDREAAAESTGHGSPLPQLKHGGPG 484

Query: 477 RAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQP 536
           RAGGGEELGG RAVKHY+QRTAVQGSPTMLAA+  + VRGA+V E  IHPFR YFE+LQ 
Sbjct: 485 RAGGGEELGGSRAVKHYLQRTAVQGSPTMLAAVVGEHVRGARVRESGIHPFRHYFEDLQI 544

Query: 537 GDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFV 596
           GDSL T RRT+TEADIVNF CLSGDHFY H D+IAA +S FG+R+ HGYFVLSAAAGLFV
Sbjct: 545 GDSLTTHRRTVTEADIVNFGCLSGDHFYMHFDEIAARQSPFGKRIAHGYFVLSAAAGLFV 604

Query: 597 DAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVF 656
               GPV+ANYGL++LRF++PV  GDTI  RLTCKRK  + ++ A  +  GVV W VEV 
Sbjct: 605 SPAPGPVLANYGLDTLRFVKPVGIGDTISARLTCKRKIDRNKKDANGQGQGVVAWDVEVS 664

Query: 657 NQHQTPVALYSILTLVARQ 675
           NQ    VA Y ILTLVA++
Sbjct: 665 NQEGELVASYDILTLVAKK 683


Lambda     K      H
   0.319    0.134    0.395 

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: 1203
Number of extensions: 42
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: 681
Length of database: 686
Length adjustment: 39
Effective length of query: 642
Effective length of database: 647
Effective search space:   415374
Effective search space used:   415374
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: 54 (25.4 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