Alignments for a candidate for paaH in Calditerrivibrio nitroreducens DSM 19672

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Calditerrivibrio nitroreducens DSM 19672

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_041723755.1 CALNI_RS01730 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000183405.1:WP_041723755.1
          Length = 791

 Score =  669 bits (1727), Expect = 0.0
 Identities = 362/793 (45%), Positives = 507/793 (63%), Gaps = 13/793 (1%)

Query: 5   IRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSRLSRQ 64
           I+KAAVLGSGVMG+ IAAHLAN GI VLLLDIVP  L  E+ KKGLT+ S E R+++ ++
Sbjct: 4   IKKAAVLGSGVMGATIAAHLANAGIKVLLLDIVPKKLDDEDLKKGLTESSKEFRNKIVKK 63

Query: 65  AMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA-LVD 123
               LL  KP+PL   +N + I  GN EDD +KL +ADW++EVVVEN+++KK +F   V 
Sbjct: 64  GYDGLLTMKPSPLFLKENINLIEIGNFEDDIQKLADADWVVEVVVENMDIKKSLFQEKVV 123

Query: 124 EHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETDPDI 183
            + K  +I+S+NTSG+SV E+A+   +D +  FL THFFNP RY+KL+EI+P + TDP I
Sbjct: 124 PNLKKDAILSTNTSGLSVNELAKVMPEDVRKRFLITHFFNPPRYMKLMEIVPNEWTDPAI 183

Query: 184 LKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITGPLI 243
            KFM  F  N LGKG+V AKDTPNFI NRIG Y +    + + + G  V E DS+TGP I
Sbjct: 184 TKFMAEFISNRLGKGIVYAKDTPNFIGNRIGVYLIFKAFKHLAELGLTVEEADSVTGPAI 243

Query: 244 GRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSKAGQ 302
           G PK+A F+  D+VG DT AH+ +N Y     DE ++V++IP F++ M+E G  G+K+ +
Sbjct: 244 GMPKTAIFKLADLVGNDTIAHIGKNSYALLTNDEERDVYQIPEFLSKMVEMGLNGNKSKK 303

Query: 303 GFYKKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRLLWN 362
           GFY K G   + LD  ++ Y    K K P+  AAKQ      ++K +++S+D+A    W 
Sbjct: 304 GFYTKNGSERFYLDLNSMEYKPLEKPKFPSTTAAKQIDDLTTRIKTVVFSNDKAAEFAWR 363

Query: 363 ITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLGADM 422
           +   TL+Y+ + + EI+DDI  +D AMKWG+ WE GPFE++DAIG+    +K ++ G  +
Sbjct: 364 VLRDTLIYTYKRIPEISDDIVNVDNAMKWGYNWEFGPFEIFDAIGVGNFVKKCDKDGVAV 423

Query: 423 PGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETKGVIAKNSG 480
           P  ++ +     E FY  ENG  +Y+D   G Y+ V ++ K+I+L+ LK+   VI  N G
Sbjct: 424 PEKLRSV-----EQFYKFENGKKYYFDIISGSYKEVVQHPKQINLEILKKGNKVIESNKG 478

Query: 481 ASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGANLA 540
           AS++DLGD V  LEFHSK N+I  DI+ M  + ++  E   + LVI NQGK F  GANLA
Sbjct: 479 ASIVDLGDGVYCLEFHSKMNSISGDILTMTKRAIKRAEEEAQALVIANQGKMFSAGANLA 538

Query: 541 MILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARIQAA 600
           M+   + +  + +++ +++ FQ+  M IKYS+ PVVAAPF + LGGG E CL A  I A 
Sbjct: 539 MLATALAEGAYDDINMMVKMFQDATMAIKYSSIPVVAAPFNVVLGGGCEYCLHADAIVAH 598

Query: 601 SEAYMGLVESGVGLIPGGGGNKELYINHLRRGH----DPMNAAMKTFETIAMAKVSASAQ 656
           +E YMGLVE GVG++P GGG KE+ I  ++       D      K F  IA AKVS SA 
Sbjct: 599 AETYMGLVEVGVGILPAGGGTKEMAIRAIQLAEKYQTDVSPFIFKFFMNIATAKVSMSAA 658

Query: 657 EAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAALLLGA 716
           E  +M+ + + D+IS+N D+L+ DAK +A +L            +K PG +  A++    
Sbjct: 659 ELYDMHYMTDKDKISMNVDNLINDAKYMALALAQNYIPKSPLVNLKAPGRSVAASIKSQL 718

Query: 717 EQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAKSQAR 776
             MK+ G I+E++  I   +A VI GG V  GT + EEYLL++EREAF+ L  + K+  R
Sbjct: 719 WNMKVGGMITEYEEFIGGLIADVITGGDVNAGTLITEEYLLKLEREAFVKLCMQKKTMER 778

Query: 777 MQHMLVKGKPLRN 789
           +QHML KGKPLRN
Sbjct: 779 IQHMLTKGKPLRN 791


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: 1407
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: 791
Length adjustment: 41
Effective length of query: 748
Effective length of database: 750
Effective search space:   561000
Effective search space used:   561000
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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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