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_2827 Ga0059261_2827 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::P07896
         (722 letters)



>FitnessBrowser__Korea:Ga0059261_2827
          Length = 683

 Score =  442 bits (1138), Expect = e-128
 Identities = 280/710 (39%), Positives = 402/710 (56%), Gaps = 54/710 (7%)

Query: 5   LRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIH 64
           L +   +A++ L  PPVNA+SP ++  + + L  A SD   KAIV+  A   F AGAD+ 
Sbjct: 10  LTVEDGVAIVTLDFPPVNAMSPALMDGLYDALMAALSDDAAKAIVLICAGRTFIAGADLK 69

Query: 65  GFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEV 124
                 P +   +L D I+   KP +AA+ G ALGGG+E AL  HYRIA   AR+GLPEV
Sbjct: 70  SLGKVQPKVDFFALQDSIENSPKPTVAALHGTALGGGMETALTFHYRIAVPSARMGLPEV 129

Query: 125 TLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPV-EEAIKF 183
            LG+LPG  GTQ LPR+ G   ALDL+ SG+ + A EAL +G++D +     + E+AI F
Sbjct: 130 NLGLLPGGGGTQRLPRITGAEAALDLLISGRQVGAKEALTIGLIDRLAAEGALREDAIAF 189

Query: 184 AQKIIDKPIEPRRIFN--KPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVK 241
           A++++D    P+RI +    V +     ++F        KQ  G+ AP+  VR ++A+V 
Sbjct: 190 AKELVDAGEPPKRIRDCEAKVAADRKDANLFERFRTSHAKQLNGLDAPQAIVRCVEAAVA 249

Query: 242 HPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGV 301
            P+E G+  E   F  L A  Q+ AL++ F AE++A K   P   +       PV+ VG+
Sbjct: 250 GPWEKGLAIERTEFQTLLAGPQSAALRHVFMAERAAQK--IPGLRA--DLPLIPVTKVGI 305

Query: 302 LGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPK 361
           +G GTMG GIA++F   G +V  VE+    LD     IT TL+   SR  +   A+ K +
Sbjct: 306 VGAGTMGSGIAMAFLAAGFAVTVVETQQAALDRGVAHITATLQ---SRVERGKLAADKAE 362

Query: 362 LRFSSST-----KELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDD 416
            + ++ T       L+  DLVVEA+FE++  K+ +F  LSA+ +P   L TNTS L+VD 
Sbjct: 363 AQIAALTPTLDLSALADADLVVEAIFENLAAKQALFGTLSAIVRPDTILATNTSFLDVDA 422

Query: 417 IASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCY 476
           IA+    P+ V+G HFFSPA+VMRLLEV+ +  +S   +A+VM+L+KK+GK  VV G C+
Sbjct: 423 IAAGAAGPERVLGMHFFSPANVMRLLEVVRAAKTSEAVLASVMALAKKLGKAAVVSGVCF 482

Query: 477 GFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQ 536
           GF+GNRMLA        ++  G  P ++D +L  FGF MGPF + DLAGLD+GW     +
Sbjct: 483 GFIGNRMLAARQVHADAMVLAGVLPWNIDRILTGFGFPMGPFAMLDLAGLDIGW-----E 537

Query: 537 GLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLS 596
           G T         V+ R           L  AGR GQK+G G+Y Y+        P P   
Sbjct: 538 GDTDS-------VKSR-----------LVAAGRKGQKSGAGYYDYENKT-----PSP-SQ 573

Query: 597 TFLSQYREVHHIEQR--TISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYG 654
           T L     +  +     T+S  EIL+R L  +INE  +ILEEG+A R   ID++++ GYG
Sbjct: 574 TALDVIAGLASVAPGSVTLSDREILDRLLLPMINEGAKILEEGIALRGSDIDLVWITGYG 633

Query: 655 WPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQG 704
           WP   GGPMF+A ++GL  V++ L+           +EP+  L +L ++G
Sbjct: 634 WPAQTGGPMFHADAIGLTRVVDGLRHM--------GVEPAALLLKLASEG 675


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: 1003
Number of extensions: 36
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 722
Length of database: 683
Length adjustment: 39
Effective length of query: 683
Effective length of database: 644
Effective search space:   439852
Effective search space used:   439852
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