Alignments for a candidate for paaH in Arcobacter nitrofigilis DSM 7299

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Arcobacter nitrofigilis DSM 7299

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_013135150.1 ARNIT_RS06725 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000092245.1:WP_013135150.1
          Length = 706

 Score =  434 bits (1116), Expect = e-126
 Identities = 254/711 (35%), Positives = 396/711 (55%), Gaps = 21/711 (2%)

Query: 9   LNVRLDN-IAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIA 67
           LN+ ++N IA +T D+   K N L  E  S++   + ++++NK+++ +V  SAKP  FIA
Sbjct: 4   LNLEINNDIATLTFDLKNTKANKLSFEVLSELNNALDEIKQNKQIKVLVIDSAKPTIFIA 63

Query: 68  GADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRV 127
           GADI  I    T +E      +G  ++ ++ AL I  IA I+GAC+GGGLELAL C  RV
Sbjct: 64  GADIKEIEAMSTEEEVYEQITKGDNILTKLEALSIPTIAYINGACMGGGLELALCCKYRV 123

Query: 128 CTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDD 187
            T + KT L  PE++LG  PG GGTQR P+L+G+ TALEMILTGK   AK+ALK+GLVD+
Sbjct: 124 ATTNEKTKLAFPEIKLGFFPGLGGTQRAPKLVGLITALEMILTGKNHDAKKALKMGLVDE 183

Query: 188 VVPHS---ILLEAAVELAKKERPSSRPLPVRERILAG-PLGRALLFKMVGKKTEHKTQGN 243
           +  +      L+  +    + +   + LP    ++      RA ++K   +  E K   +
Sbjct: 184 IFDNGQKEFKLKEFITKVLENKVQRKKLPFVNNLMEKFSFTRAYIYKKSLQGIEKKVNRD 243

Query: 244 YPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGSDA 303
           + A    LEV++    +    G D EARAF +LA T +S+ +  +FF    + K+   + 
Sbjct: 244 FKAPYTALEVIQNTFTESFEKGIDIEARAFSQLAATKESKYMIELFFMFEKLNKN--FEK 301

Query: 304 PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRR 363
            P P+++V +LG G+MG GI ++ + K    +RIK    +  N  +K      +  ++RR
Sbjct: 302 TPTPISNVAVLGNGVMGKGIIWLFS-KFLNEIRIKIRKIEQANDIIKDVAKLYDSSIKRR 360

Query: 364 HLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASN 423
            +  ++ D +L  IS T  + G     L +EA+ EN   K++   E+E+      I A+N
Sbjct: 361 TMSQNQVDFKLNKISYTDKFNGLGQTQLALEAIIENENAKKEAFKELEEVLDKDAIIATN 420

Query: 424 TSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKT 483
           TSS+ I  + +     +  +G+HFF+PV  MPLVE+IP + TS +TI   ++L    GKT
Sbjct: 421 TSSISIEKLGSELKNKKNFLGIHFFNPVNMMPLVEVIPSSHTSKKTINRVIELLTTCGKT 480

Query: 484 PIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDT 543
           PIVV D AGF VNRIL PYINEA  +L +G  ++ ID  L  FG P+GP  L D VGID 
Sbjct: 481 PIVVGDCAGFIVNRILLPYINEAAFILEEGSDIKTIDKILKDFGLPMGPFILADTVGIDI 540

Query: 544 GTKIIPVLEAAYGERFSAPANVVSSILNDDR-KGRKNGRGFYLYGQKGRKSKKQVDPAIY 602
           G K+  +L+ +YG R +  A +++ +  D +  G+K  +GFYL+  K  +  ++V   + 
Sbjct: 541 GFKVATILQESYGSRMTV-APILTKVYKDLKLLGKKAKKGFYLHNTKNLEINEEVTKLL- 598

Query: 603 PLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGP 662
               +  +   +  ++ ERC+ +M+NEA RC++E ++   +  D   + G GFPP+ GG 
Sbjct: 599 ----STNRKEFTQKEIIERCMFIMVNEASRCLEEGIVNDPKIIDFAMITGTGFPPYKGGI 654

Query: 663 FRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGAR------GESFWK 707
             Y + +G   +V  +++    +G RF P   L ++         GE  WK
Sbjct: 655 CAYANDMGISYIVDELKQYEKVFGERFKPSLLLEKLDKENKDFKTGEELWK 705


Lambda     K      H
   0.319    0.137    0.393 

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: 918
Number of extensions: 35
Number of successful extensions: 6
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: 714
Length of database: 706
Length adjustment: 39
Effective length of query: 675
Effective length of database: 667
Effective search space:   450225
Effective search space used:   450225
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: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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