Alignments for a candidate for paaH in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Herbaspirillum seropedicae SmR1

Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate HSERO_RS20645 HSERO_RS20645 3-hydroxyacyl-CoA dehydrogenase

Query= reanno::Marino:GFF2749
         (506 letters)



>FitnessBrowser__HerbieS:HSERO_RS20645
          Length = 512

 Score =  458 bits (1178), Expect = e-133
 Identities = 250/498 (50%), Positives = 325/498 (65%), Gaps = 8/498 (1%)

Query: 3   ALDTQTKVAVVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGK 62
           AL     VAV+G+G MG+GIAQVAA AGH V L+D REGAA      I   L + V K K
Sbjct: 9   ALSRSALVAVIGSGTMGAGIAQVAAVAGHPVLLYDSREGAAGKAIGAICTNLDKLVSKDK 68

Query: 63  MQQQELDDVIGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNT 122
           +          RI     L+++  A LVIEAI+E L  K +L   LE + +   ILATNT
Sbjct: 69  LTPALAQAASQRISVAQSLEELHQADLVIEAIVEQLAAKHELFGKLEAIVSTRCILATNT 128

Query: 123 SSISVTALGADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKP 182
           SS+S+T + A +  PER+VGMHFFNP P+MALVE++ GLA+   +A  +H TA AWGK P
Sbjct: 129 SSLSITQIAAGLQHPERVVGMHFFNPVPMMALVEIISGLASDAALAQCLHDTALAWGKTP 188

Query: 183 VYATSTPGFIVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHD 242
           V A STPGFIVNR+ARP+YAE LR+L E     AT+DA++REAG FRMG FEL DLIGHD
Sbjct: 189 VMARSTPGFIVNRLARPYYAEGLRMLHEGGAQPATIDAVMREAGGFRMGPFELMDLIGHD 248

Query: 243 VNYAVTSSVFNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQPKTEPAH 302
           VN+AVT SVF++Y+ DPRF PSLIQ+ELV AG LGRKSG+GFY YGE+A  P+P+TE  +
Sbjct: 249 VNFAVTQSVFHAYFNDPRFTPSLIQQELVHAGYLGRKSGRGFYRYGEAAGAPRPETERDY 308

Query: 303 QSDESVIIAEGNPGVAAPLLERLKAAGLTIIERD--GPGQI--RFGDAVLALTDGRMATE 358
               +     G+     PL+E +       ++R    P Q+  +   A L +TDGR AT 
Sbjct: 309 PKPTATPQLYGD----HPLVEMIHTRYPGQVQRHPARPDQLLMKVNAACLCITDGRSATL 364

Query: 359 RAACEGVANLVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPG 418
           RA      +LVL DLA DY+ A+RLALA ADQ      +    +LQ  G+++S + D PG
Sbjct: 365 RAWEHQEPDLVLVDLALDYADATRLALAKADQCRPQRYAEVAGVLQACGLDLSPMQDVPG 424

Query: 419 LVIMRTVAMLANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTN 478
           +++MRTV ML NEAADA   GV   AD D+AM+ G+NYP GPL+W++ +G   V +VL +
Sbjct: 425 MMVMRTVCMLVNEAADAVNQGVCNAADADMAMRKGVNYPRGPLAWANEIGIDTVNQVLHH 484

Query: 479 IQTSYAEDRYRPALLLRK 496
           +  +Y EDRYR + LL++
Sbjct: 485 LCATYGEDRYRISPLLQR 502


Lambda     K      H
   0.318    0.133    0.375 

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: 661
Number of extensions: 26
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: 506
Length of database: 512
Length adjustment: 34
Effective length of query: 472
Effective length of database: 478
Effective search space:   225616
Effective search space used:   225616
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 (21.7 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)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources