Alignments for a candidate for paaH in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Hydrogenophaga taeniospiralis NBRC 102512

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_068167433.1 HTA01S_RS04710 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_001592305.1:WP_068167433.1
          Length = 799

 Score =  966 bits (2498), Expect = 0.0
 Identities = 501/809 (61%), Positives = 600/809 (74%), Gaps = 12/809 (1%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           M+ F VKKVAVLGAGVMGAQIAAHL+N +VPVVLFDLPAKEG KNGI  RA+ENLKKL P
Sbjct: 1   MNRFQVKKVAVLGAGVMGAQIAAHLVNVKVPVVLFDLPAKEGHKNGIVTRAVENLKKLKP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           +PLG+  +A LI  ANYE+ +  LK+CDL+IEAIAERMDWK DLY K+AP +A HAI A+
Sbjct: 61  SPLGVAADADLIGQANYEEHMEQLKDCDLIIEAIAERMDWKLDLYTKIAPFIAPHAIVAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSIT LS+     +K RFCG+HFFNPPRYM LVELI T TT+PQILD LE F+T+ 
Sbjct: 121 NTSGLSITKLSEVLPEAIKPRFCGIHFFNPPRYMTLVELIATPTTEPQILDDLETFVTSG 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVVRAKDTPNF+ANR+GI  +LA   E E FG+ +DVVDDLTG +LGRA S TFRTA
Sbjct: 181 LGKGVVRAKDTPNFVANRIGIAGMLATMKEVENFGLTYDVVDDLTGKRLGRASSGTFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHD--DPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKA 298
           DVVGLDTMAHV+KT+QD L D  DPF   + TP VLK L++ G LGQK  AGF+KK G+ 
Sbjct: 241 DVVGLDTMAHVVKTLQDNLDDSTDPFYGSFGTPPVLKKLIEMGNLGQKAKAGFFKKVGRD 300

Query: 299 IKVLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358
           I+  D  +G+YV AG+KADE+  RMLK+ AAER+KLLR +  PQ QFLWA+ R+ FHY A
Sbjct: 301 IQRFDLASGEYVPAGEKADEVYGRMLKRPAAERLKLLRNAEGPQGQFLWAILRNSFHYAA 360

Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418
           V+L  IA +A D+D A+RWGFG   GPFE WQ AGW +VA+ ++ED+ AGKALS APLP 
Sbjct: 361 VHLATIAETARDVDQAMRWGFGMKQGPFELWQEAGWLEVAKMIQEDIAAGKALSTAPLPE 420

Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTV 478
           WVF+GPVAE  GVH A GSW+P+   F  R +LPVYQRQ F   + G A      AG T+
Sbjct: 421 WVFKGPVAEAGGVHTAQGSWNPSKGEFQGRLQLPVYQRQHFPELLLGEAGPKFETAGTTI 480

Query: 479 EENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538
           EENDA+RIW  +G  DVL+ S K+KM+ I PDV +GL  AIDLAE  Y+GLVVW      
Sbjct: 481 EENDAIRIWSLDG--DVLIASIKTKMHAISPDVCEGLMAAIDLAEKEYQGLVVWSGDE-- 536

Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598
                 PFSAGA+L+A +PAFM  G   IE      Q  M+R++YA+VPVVSA  G+ALG
Sbjct: 537 ------PFSAGADLQAMLPAFMAVGVSAIEDAEGFMQQTMLRLRYANVPVVSAVRGLALG 590

Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLT 658
           GGCEL ++SA RV  +E+YIGLVEVGVGLVP  GGL   A  AA  A+ +   ++L FLT
Sbjct: 591 GGCELAVYSARRVVHMESYIGLVEVGVGLVPGAGGLTYIARRAAENAETSTGKDLLPFLT 650

Query: 659 SRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPTL 718
             F +AAMAKV  SALE+R++GY+  SD IV +  ELL+VA +E ++L + GYRAP   L
Sbjct: 651 EGFTAAAMAKVGTSALESRKLGYVLHSDVIVPHKDELLFVAISEAKSLFNGGYRAPHKRL 710

Query: 719 VPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALE 778
            PVAGR G ATI  SLVNMRDGGFIS HDF IAS IA  V GGDVE G+LV+ED+L+ LE
Sbjct: 711 FPVAGRDGKATILGSLVNMRDGGFISQHDFHIASLIANVVTGGDVEPGTLVNEDYLMTLE 770

Query: 779 RKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           R+AF  L+   KTQERI+GML TGKPVRN
Sbjct: 771 RRAFCSLIVHAKTQERILGMLNTGKPVRN 799


Lambda     K      H
   0.319    0.134    0.391 

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: 1656
Number of extensions: 64
Number of successful extensions: 4
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: 807
Length of database: 799
Length adjustment: 41
Effective length of query: 766
Effective length of database: 758
Effective search space:   580628
Effective search space used:   580628
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 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