Alignments for a candidate for paaH in Croceitalea dokdonensis DOKDO 023

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Croceitalea dokdonensis DOKDO 023

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_054557393.1 I595_RS00285 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_001306415.1:WP_054557393.1
          Length = 801

 Score =  718 bits (1854), Expect = 0.0
 Identities = 386/802 (48%), Positives = 517/802 (64%), Gaps = 14/802 (1%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M +HI K AV+GSG+MGSGIA H ANIG+ VLLLDIVP +L  +E+ KGLT D + VR+R
Sbjct: 1   MKRHINKIAVIGSGIMGSGIACHFANIGVEVLLLDIVPRELNAKEKAKGLTLDDTTVRNR 60

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           +   ++   LK KP+P+   K  + IT GNLEDD  K+ + DWIIEVVVE L++KK++F 
Sbjct: 61  IVNDSLAAALKSKPSPVYHQKFANRITTGNLEDDIAKVAKVDWIIEVVVERLDIKKQVFE 120

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            ++ HR  G++++SNTSGI +  M+EGRSDDF+ HF GTHFFNPARYLKL EIIP  +T 
Sbjct: 121 TLERHRTPGTLITSNTSGIPIHFMSEGRSDDFQKHFCGTHFFNPARYLKLFEIIPGPKTS 180

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
           P++L F+  +GE  LGK  V AKDTP FI NRIG + +      +   G  V EVD +TG
Sbjct: 181 PEVLVFLNGYGEQFLGKTSVLAKDTPAFIGNRIGIFSIQSLFHALKALGMTVEEVDKLTG 240

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDEK-EVFRIPSFMNDMLEKGWIGSK 299
           P+IGRPKSATFRT+DVVGLDT  HVA  + +    DE+ E+F +P F+  M+E  W+GSK
Sbjct: 241 PVIGRPKSATFRTVDVVGLDTLVHVANGISENCKDDERHELFALPDFIATMMENKWLGSK 300

Query: 300 AGQGFYKK----EGKT-IYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354
            GQGFYKK    +GKT I  LD  T+ Y  +   K P LE  K       +   L    D
Sbjct: 301 TGQGFYKKSKDAKGKTEILTLDLDTMEYRSKKSAKFPTLEQTKTIDTVVDRFAVLTAGTD 360

Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414
           +AG        Q   Y +  + EI+D+++ ID AMK GFGWE GPF++WDAIGL +  E 
Sbjct: 361 KAGEFYRKSFGQLFAYVSHRIPEISDELYKIDDAMKAGFGWEHGPFQIWDAIGLDKGLEF 420

Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYDRGEYRAVK--ENKKRIHLQALKETK 472
           +     +   W+ EM   G  +FY  ++G  ++YD    + VK       I L  ++ TK
Sbjct: 421 IAAEKQEAAAWVSEMKTAGITSFYQVKDGATYFYDIPSKQMVKVPGQDAFIILDNIRTTK 480

Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532
            V  KN+G  + DLGD +   EF SK N IG D++  ++K ++  E++++GLV+GNQ  N
Sbjct: 481 EVF-KNAGVVIEDLGDGILNCEFQSKMNTIGADVLAGLNKAIDLAEKDFQGLVVGNQAAN 539

Query: 533 FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACL 592
           F VGAN+ MI M   +  + E++  I+ FQ++MM+++YS+ P VAAP GMTLGGG E  L
Sbjct: 540 FSVGANIGMIFMMAVEQEYDELNMAIKMFQDSMMRMRYSSIPTVAAPHGMTLGGGCELSL 599

Query: 593 PAARIQAASEAYMGLVESGVGLIPGGGGNKELYI---NHLRRGHDPMNAAMKTFETIAMA 649
            A ++ AA+E YMGLVE GVG+IPGGGG+KEL +   +  R+G   +N   + F TI MA
Sbjct: 600 HADKVVAAAETYMGLVEFGVGVIPGGGGSKELAMRASDSFRKGDVELNVLQEYFLTIGMA 659

Query: 650 KVSASAQEAREMNIL-KETDQISVNQDHLLYDAKQLAASLYDTGW-RPPVKEKVKVPGET 707
           KVS SA EA ++ +L K  D + VN+D  +  AK  A  + + G+ RPP ++ VKV G+ 
Sbjct: 660 KVSTSAYEAYDLGLLQKGKDIVVVNKDRQIATAKAHAKLMAEAGYTRPPARKDVKVLGKQ 719

Query: 708 GYAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSL 767
                L+G + M+ S YISEHD KIA KLAYV+AGG +   T V E+YLL+IEREAFLSL
Sbjct: 720 ALGMFLVGTDSMEASNYISEHDKKIANKLAYVMAGGDLSEPTMVSEQYLLDIEREAFLSL 779

Query: 768 SGEAKSQARMQHMLVKGKPLRN 789
             E K+  R+QHML  GKPLRN
Sbjct: 780 CTERKTLERIQHMLKTGKPLRN 801


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: 1487
Number of extensions: 69
Number of successful extensions: 7
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: 801
Length adjustment: 41
Effective length of query: 748
Effective length of database: 760
Effective search space:   568480
Effective search space used:   568480
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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