Alignments for a candidate for paaH in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Desulfatibacillum aliphaticivorans DSM 15576

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_028316415.1 G491_RS0124405 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000429905.1:WP_028316415.1
          Length = 802

 Score =  686 bits (1770), Expect = 0.0
 Identities = 375/808 (46%), Positives = 524/808 (64%), Gaps = 25/808 (3%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M + IRKAAVLGSGVMG GIAA LA+ GI  LLLDIVP DLT EE      K+  + R+R
Sbjct: 1   MVRRIRKAAVLGSGVMGGGIAALLASAGIKTLLLDIVPFDLTDEE------KNDPKARNR 54

Query: 61  LSRQAMKKLLKQKPAPLTSAKNT-SYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIF 119
           + +     ++K KP+   +AK+  + +  GN EDD +KL E DWI+EVVVENL++K+++ 
Sbjct: 55  IVQAGFDGIVKSKPSLFMNAKDEKALVQVGNFEDDWDKLAECDWIVEVVVENLKIKQEVL 114

Query: 120 ALVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKET 179
           A V++ RK  +IVS+NTSGI ++ M++  S +F+ +F+GTHFFNP RY+KLLE+IP  ET
Sbjct: 115 AKVEKVRKADAIVSTNTSGIPLEAMSKELSSEFRQNFMGTHFFNPVRYMKLLELIPGAET 174

Query: 180 DPDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSIT 239
            P++L FM  FGE +LGKG+V AKDTPNFI NRIG  G++  +Q M++ G  + EVD++ 
Sbjct: 175 KPEVLDFMKDFGERILGKGIVWAKDTPNFIGNRIGVQGMVQAMQLMVEDGMSIPEVDALF 234

Query: 240 GPLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGS 298
           GP++GRPK+A F+T D+VGLDT  HVA N Y+    DE +E F++P F++ M+EK  +G+
Sbjct: 235 GPVLGRPKTAMFKTADLVGLDTLGHVASNTYELVVDDEARETFKVPEFVSQMIEKKMLGN 294

Query: 299 KAGQGFYKK----EGKTIYE-LDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSD 353
           K   GFYKK    E K I + L+P T+ Y E  +   P L+AAK AKG   K+KA+ Y+D
Sbjct: 295 KTKGGFYKKDMTPEWKLIPKVLNPQTMEYEEFERPTFPCLDAAKSAKGLAEKIKAVAYAD 354

Query: 354 DRAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAE 413
           D+ G+ +W + S  L+Y+A  + EI+D I  ID +MKWG+ +  GPFE WDA+G+K+S  
Sbjct: 355 DKGGKFVWKVLSNGLIYAANRIPEISDTIVEIDNSMKWGYNFTFGPFETWDALGVKESVA 414

Query: 414 KLEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKET 471
           K+E  G  +P  +K+ML  G E+FY  ENG  +Y+D   GEY+A++ +   I L+ LK  
Sbjct: 415 KMEAEGMTVPENVKKMLAAGVESFYKFENGIDYYFDFATGEYKAIELSPTIISLKGLKGA 474

Query: 472 KGVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGK 531
              +  N+  SL+DL D V  +EFH+K NAI  +++  + + L   + N  G+VIGNQ  
Sbjct: 475 GKKVMGNNSVSLVDLEDGVFCVEFHTKMNAINAELVDGMGEALAYVDDNGIGVVIGNQSP 534

Query: 532 N----FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGG 587
                F  G +LA +L   +   + ++D  + R Q  MM   YS+ PVVAAPFGMTLGGG
Sbjct: 535 GFPGAFSAGGDLAYMLGLAKAGKYADIDAFLARAQGGMMNALYSSFPVVAAPFGMTLGGG 594

Query: 588 TEACLPAARIQAASEAYMGLVESGVGLIPGGGGNKELYINHLR------RGHDPMNAAMK 641
            E CL A +I A SE +MGLVE GVGLIPGGGG    +           + +D +   M 
Sbjct: 595 CETCLAADKIVAHSELFMGLVEVGVGLIPGGGGCMNTWKKFALSTPPCVKVNDLLPYFMH 654

Query: 642 TFETIAMAKVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKV 701
            F+ IAMAK S SA +AR M  L   D+I +N+D+L+ +AK+    + D G+ PP K+ +
Sbjct: 655 VFQNIAMAKFSNSAAQARTMGFLGPKDRIVMNRDYLIGEAKKEVLRMVDAGYAPPQKKPI 714

Query: 702 KVPGETGYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIER 761
            V G++           M  +GYISEHD  IAKK+AY+I GG V   + VDE+Y+L++ER
Sbjct: 715 PVLGKSAQGLADQQLFDMLAAGYISEHDALIAKKVAYIIGGGDVRDNSTVDEDYILKLER 774

Query: 762 EAFLSLSGEAKSQARMQHMLVKGKPLRN 789
           +AF+SL  E K+ AR++HML  GKPLRN
Sbjct: 775 DAFVSLFKEEKTIARVEHMLATGKPLRN 802


Lambda     K      H
   0.316    0.134    0.382 

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: 1504
Number of extensions: 66
Number of successful extensions: 8
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: 789
Length of database: 802
Length adjustment: 41
Effective length of query: 748
Effective length of database: 761
Effective search space:   569228
Effective search space used:   569228
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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