Alignments for a candidate for paaH in Desulfoscipio geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Desulfoscipio geothermicus DSM 3669

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_092482981.1 BM299_RS08140 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_900115975.1:WP_092482981.1
          Length = 807

 Score =  813 bits (2100), Expect = 0.0
 Identities = 423/807 (52%), Positives = 557/807 (69%), Gaps = 18/807 (2%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M + I KAAVLG+GVMG+ IAAHLAN+GIP  LLDIVPN LT EEEKKGLT +S +VR+R
Sbjct: 1   MKRSINKAAVLGAGVMGATIAAHLANVGIPTYLLDIVPNQLTPEEEKKGLTLESPQVRNR 60

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           L+  A+  +LK KPAP    +N + +TPGN ED+ + L E DWIIEVVVE L++K+ +F 
Sbjct: 61  LATGAIGAMLKAKPAPFYVPENAALLTPGNFEDNMDVLAECDWIIEVVVERLDIKQSLFK 120

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            V+  R+ GSIV+SNTSGIS+ +M EG S +FK HFLG HFFNP RY+KLLE+IP  ET 
Sbjct: 121 KVEAVRRPGSIVASNTSGISINKMCEGLSQEFKQHFLGAHFFNPPRYMKLLELIPCSETL 180

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
           P++L+FM  FGE +LGKGVV  KDTPNFIANRIG YG+  T++ ML  G  V EVD++TG
Sbjct: 181 PEVLEFMRDFGERILGKGVVICKDTPNFIANRIGVYGMCATIKAMLDFGLTVEEVDALTG 240

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKA-DGDEKEVFRIPSFMNDMLEKGWIGSK 299
             + RPKSA+FRTLD+VGLD   HVA+NVYD A +  EK VF  P F+  MLE  W+G K
Sbjct: 241 RALCRPKSASFRTLDMVGLDVMVHVAKNVYDVATEPAEKAVFETPEFLQKMLENKWLGDK 300

Query: 300 AGQGFYKK----EGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDR 355
             QGFYKK    +G+ I  LD   + Y  + K K  +LEAAKQA     +MK L++  D+
Sbjct: 301 TKQGFYKKVKTDKGREILVLDYNAMEYRPKEKPKFASLEAAKQAGKPAKQMKTLVFGKDK 360

Query: 356 AGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKL 415
                W +  +T++Y+A LLGEIADDI +ID AMKWGF W+ GPFE+WD +G+++ A+++
Sbjct: 361 GAEFAWRVQKETIVYAANLLGEIADDIQSIDDAMKWGFNWDFGPFEVWDILGVQEVADRI 420

Query: 416 EQLGADMPGWIKEMLDKGNETFYIKENGTVFYYDRGEYRAVKEN--KKRIHLQALKETKG 473
           +  G  +P  ++E+L  G   FY K++G  +Y+++    +V+E   +  I L  LKE   
Sbjct: 421 KAEGGTVPKVVEELLAAGRTGFYEKKDGYRYYFEQNSKESVRERIPEGIIFLAPLKEQNK 480

Query: 474 VIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNF 533
           VI  NSGASLID+GD VA LEFHSK+NAIG DI+ MI+  ++E E+NY+GLVIGN G++F
Sbjct: 481 VIKSNSGASLIDIGDGVACLEFHSKANAIGDDIVNMINYSVKEVEQNYEGLVIGNFGQHF 540

Query: 534 CVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLP 593
            VGANL +ILME +DD F E+D ++  FQ+  M++KY  KPVVAAP GMT+GGG E CL 
Sbjct: 541 SVGANLFLILMEAEDDEFDELDIMVDEFQKANMRLKYCKKPVVAAPHGMTVGGGCEVCLH 600

Query: 594 AARIQAASEAYMGLVESGVGLIPGGGGNKELYI---------NHLRRGHDPMNAAM--KT 642
           A R+ AA E YMGLVE GVGL+PGGGG KEL           + +  G       M  + 
Sbjct: 601 AHRVNAAGETYMGLVEVGVGLVPGGGGCKELAFRAAELMPPKSQVTTGGTNTVQPMINRA 660

Query: 643 FETIAMAKVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVK 702
           FE IAMAKV+ S  EA +   ++ TD++S N+D ++ DAK++   +   G++P   +K++
Sbjct: 661 FENIAMAKVATSGYEAIKFGYMRPTDRVSPNRDRIIGDAKRMVLQMAANGFKPLQPKKMQ 720

Query: 703 VPGETGYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIERE 762
             G  GYAA+ LG + +     ISEHD KIAKK+AY++ GG V  GTEV E+ LL++ERE
Sbjct: 721 AVGNAGYAAIELGIQTLLWGKQISEHDAKIAKKVAYILTGGGVTPGTEVTEQDLLDLERE 780

Query: 763 AFLSLSGEAKSQARMQHMLVKGKPLRN 789
           AFLSL GE K+  RM++ML   KPLRN
Sbjct: 781 AFLSLLGEPKTLDRMRYMLKYNKPLRN 807


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: 1520
Number of extensions: 54
Number of successful extensions: 5
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: 807
Length adjustment: 41
Effective length of query: 748
Effective length of database: 766
Effective search space:   572968
Effective search space used:   572968
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 Apr 09 2024. 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 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