Alignments for a candidate for ech in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Cupriavidus basilensis 4G11

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate RR42_RS22630 RR42_RS22630 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::P07896
         (722 letters)



>FitnessBrowser__Cup4G11:RR42_RS22630
          Length = 696

 Score =  561 bits (1445), Expect = e-164
 Identities = 318/699 (45%), Positives = 432/699 (61%), Gaps = 26/699 (3%)

Query: 11  LAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFT 70
           +A++ L NPPVN +  TV   + +G+ +A  D  V AIVI GA   FC GADI  F+A  
Sbjct: 12  IAILLLDNPPVNGLGDTVRLGLFDGIAQATQDDAVAAIVILGAGKVFCGGADIRQFNAPA 71

Query: 71  PGL--ALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGI 128
                 L  ++  I++  KPV+AAI GVALGGG+ELALGCHYRIA+A A +GLPEV LG+
Sbjct: 72  ASAQPTLRQVIARIEQSAKPVVAAIHGVALGGGMELALGCHYRIASADASLGLPEVNLGL 131

Query: 129 LPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKII 188
           +PG  GTQ LPR++GVP AL+LI  GK +  D+A+ LG+ DA++  DP+  A+ FA+++ 
Sbjct: 132 VPGGGGTQRLPRLIGVPAALELIQGGKPVRGDKAVALGMADALIDGDPLAAAMAFAERVA 191

Query: 189 DKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGI 248
             P     I  +P      +D  FA   A V  +    LA    +  +QA+ + P + G+
Sbjct: 192 GLPGAHPVIARRPCADAAGVD--FAARSAAVSAKARNALAQRAAIACVQAATRLPIDAGL 249

Query: 249 KEEEKLFMYLRASGQAKALQYAFFAEKSANKWST-PSGASWKTASAQPVSSVGVLGLGTM 307
            +E   F  L AS ++KAL++ FFAE+ A K +  P+GAS +T     V+ VG+LG GTM
Sbjct: 250 DDERARFDQLVASTESKALRHLFFAEREAPKVAALPAGASLRT-----VARVGILGAGTM 304

Query: 308 GRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPKLRFSSS 367
           G GIA++FA  GI+V  +E     LD    +I    E  A++     Q  A+     + +
Sbjct: 305 GAGIAMAFANAGIAVTLLEQQQAALDRGLAMIRRNYEITAAKGKLTAQEIAQRMACITPT 364

Query: 368 TKE--LSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQ 425
             +  L+  DLV+EAVFEDM +KK VFA L ALCKPGA L TNTS L++D IA+ST RPQ
Sbjct: 365 LADAALADADLVIEAVFEDMAVKKAVFARLDALCKPGAILATNTSRLSIDVIAASTSRPQ 424

Query: 426 LVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLA 485
            VIG HFFSPA+VM+LLEV+    ++P  IAT M +++ IGKI V+V  C GFVGNRML 
Sbjct: 425 DVIGLHFFSPANVMKLLEVVQGERTAPEVIATCMKMARAIGKIPVLVRVCEGFVGNRMLT 484

Query: 486 PYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPP 545
           PY+ +  FLLEEG+ P+ VDG L  FG  MGP  ++DLAG+D+ W  RK    T P+   
Sbjct: 485 PYWREAGFLLEEGASPQQVDGALTRFGMAMGPLAMADLAGMDINWATRKRLAPTRPA--- 541

Query: 546 GTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREV 605
                   + RYS + D +CE GRFGQKT  G+Y+Y+    R   PDP +   +      
Sbjct: 542 --------HLRYSKVADRICEQGRFGQKTNAGYYRYEAG-SRAPLPDPAVDALIRACAAE 592

Query: 606 HHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFY 665
             IE+R +S EEI+ERC+ +L NE  RILEEG+A R   IDV+Y+HGYG+P  +GGPMF+
Sbjct: 593 AGIERREVSDEEIVERCMLALANEGARILEEGIARRAADIDVVYVHGYGFPAWRGGPMFH 652

Query: 666 AASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQG 704
           A ++GL   LEK++     + +     P+  L RLVAQG
Sbjct: 653 AETIGLGRTLEKIRALNAIHGE--HWTPAPLLVRLVAQG 689


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: 1096
Number of extensions: 40
Number of successful extensions: 8
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: 696
Length adjustment: 39
Effective length of query: 683
Effective length of database: 657
Effective search space:   448731
Effective search space used:   448731
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: 55 (25.8 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)
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