Alignments for a candidate for ech in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Sphingomonas koreensis DSMZ 15582

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Ga0059261_0837 Ga0059261_0837 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::P07896
         (722 letters)



>FitnessBrowser__Korea:Ga0059261_0837
          Length = 676

 Score =  464 bits (1194), Expect = e-135
 Identities = 271/667 (40%), Positives = 381/667 (57%), Gaps = 33/667 (4%)

Query: 18  NPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFTPGLALGS 77
           NPPVNA+   V + +   +++   D ++KA VI      F AGADI  F       +L  
Sbjct: 20  NPPVNALGAAVRQGLDAAIKELAGDDSLKAAVIRCDGRTFFAGADITEFGKPMQEPSLPV 79

Query: 78  LVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQL 137
           LVD I+  +KPV+AA+ G ALGGG E+AL CHYRIA   A+ GLPEV LGILPGA GTQ 
Sbjct: 80  LVDLIEASEKPVVAAVHGTALGGGCEVALACHYRIAVPSAKFGLPEVKLGILPGAGGTQR 139

Query: 138 LPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVE-EAIKFAQKIIDKPIEPRR 196
           LPRV GV  AL+L T G  +SA  A   G++D +   D +  +AI +A +I      PR 
Sbjct: 140 LPRVGGVEFALELATKGDPVSASAAKDAGLVDRLAGEDSLTADAIAYANEIAAARPLPRT 199

Query: 197 IFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGIKEEEKLFM 256
              KPV     +   F +  AK   ++  + AP   +  I+ +   PY  G++ E   FM
Sbjct: 200 S-EKPVTVEAGVFEAFRKTNAK---RFRNMDAPAEIIAVIEETAGKPYAEGVQRERMGFM 255

Query: 257 YLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGTMGRGIAISFA 316
            L    Q+ AL++ FFAE+ A K         +    +P+  VGV+G GTMG GI+++F 
Sbjct: 256 KLIMGAQSAALRHIFFAERKAAKIDDVP----EDTKLRPIKRVGVIGAGTMGGGISMNFL 311

Query: 317 RVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQA--SAKPKLRFSSSTKELSTV 374
             GI V   E   + LD     I    E  A++     +    A   L+ +    +L+  
Sbjct: 312 SAGIPVTIAEMQQEALDRGTGTIRKNYEATAAKGRMTAEQVEGAMGLLKSTLDLNDLAEC 371

Query: 375 DLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFS 434
           DL++EAV+E+M++KK +F +L  + KPGA L +NTS L++D+IAS+T RP  V+G HFFS
Sbjct: 372 DLIIEAVYENMDVKKDIFGKLDKIAKPGAILASNTSYLSIDEIASATGRPGDVVGMHFFS 431

Query: 435 PAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFL 494
           PA++M+LLEV+    +    +ATVM L+KKI K+ VV G CYGF+GNRML P   +   L
Sbjct: 432 PANIMKLLEVVRGAKTDKDVLATVMDLAKKIKKVAVVAGVCYGFIGNRMLIPRQMEAMKL 491

Query: 495 LEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTPVRKRGN 554
           L EG+ P  VD V  EFG  MGPF++SDLAG+D+GW                     R  
Sbjct: 492 LHEGATPMQVDKVHVEFGMPMGPFQMSDLAGVDIGW--------------------HRDP 531

Query: 555 SRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREVHHIEQRTIS 614
           +R   + D L    R+GQKT  G+Y YD    R   P P ++  + ++R      Q  ++
Sbjct: 532 TRIENIRDALAAENRWGQKTKAGFYDYDDK--RNPSPSPRVAEIIEEFRTKTGTPQHEVT 589

Query: 615 KEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFYAASVGLPTV 674
            EEI+ER  Y+++NE  +ILEEGMA R   IDV++++GYGWP ++GGPMF+A  VGL T+
Sbjct: 590 DEEIMERTFYTMVNEGAKILEEGMAQRASDIDVVWIYGYGWPPYRGGPMFWADQVGLKTI 649

Query: 675 LEKLQKY 681
           +  L+K+
Sbjct: 650 VAGLEKH 656


Lambda     K      H
   0.319    0.136    0.405 

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: 1091
Number of extensions: 60
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: 722
Length of database: 676
Length adjustment: 39
Effective length of query: 683
Effective length of database: 637
Effective search space:   435071
Effective search space used:   435071
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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)
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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