Alignments for a candidate for ech in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Tistlia consotensis USBA 355

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_085121628.1 B9O00_RS06390 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::P07896
         (722 letters)



>NCBI__GCF_900177295.1:WP_085121628.1
          Length = 707

 Score =  523 bits (1347), Expect = e-152
 Identities = 294/698 (42%), Positives = 427/698 (61%), Gaps = 28/698 (4%)

Query: 11  LAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFT 70
           +A++ + NPPVNA+   V   +   L++A +D  VKA+V+ GA   F  GADI  F    
Sbjct: 20  VAVVTIANPPVNALGYAVRSGIVAALERAAADPAVKAVVLTGAGRTFSGGADITEFGKPP 79

Query: 71  PGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILP 130
               L +++   +   KPV+AAI+GVALGGGLELAL CH R+A   AR+GLPEV LG+LP
Sbjct: 80  REPGLSAVIRHCESLAKPVVAAIRGVALGGGLELALACHARVAAPDARLGLPEVKLGLLP 139

Query: 131 GARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDK 190
           GA GTQ LPRVVG   A+++I +G  ++A +A  LG++D +V+ D V  A   A+ +++ 
Sbjct: 140 GAGGTQRLPRVVGPEAAVEMIVTGTPIAAAKAATLGLVDGIVEDDLVAGATAHARALVES 199

Query: 191 PIEPRRIFNKP--VPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGI 248
              P  + ++   + +     S F     ++ ++  G+ AP  CVR+++ ++  P++  +
Sbjct: 200 RQTPVPVRDREDRLAATRRDPSAFEAKAKQLTQRTRGLEAPLACVRAVRMALDTPFDEAL 259

Query: 249 KEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGTMG 308
             E  LF  L    Q+KA ++ FFAE+ A K +       +  + +PV+ VGV+G GTMG
Sbjct: 260 SRERALFTELLDGFQSKAQRHLFFAEREATKVAGVG----REVTPRPVARVGVVGAGTMG 315

Query: 309 RGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPKLRFSSST 368
            GIA++FA  GI V  VE + + L+    +I    +   +R     Q   +     + ST
Sbjct: 316 GGIAMTFANAGIPVTLVEMNREALERGLGVIRKNYDLSVARGSLGEQERDRRLALITGST 375

Query: 369 K--ELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQL 426
           +  +L+  DLV+EAVFE+M +KK+VF  L  + +PGA L +NTS L++D IA +T RP  
Sbjct: 376 RYEDLAVADLVIEAVFEEMAVKKEVFGRLDRIARPGAILASNTSYLDIDAIADATGRPAD 435

Query: 427 VIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAP 486
           V+GTHFFSPA+VM+LLE++  R ++P  +AT++ L+K+IGK+ VVVG C+GFVGNRMLA 
Sbjct: 436 VVGTHFFSPANVMKLLEIVRGRRTAPDVLATLLGLAKRIGKVPVVVGVCHGFVGNRMLAA 495

Query: 487 YYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPG 546
              +   LL EG+ P++VD    +FGF MGPF + DLAGLDVGW+ RK  G         
Sbjct: 496 RSAENEALLLEGALPQEVDRAFTDFGFPMGPFAMGDLAGLDVGWRNRKSLG--------- 546

Query: 547 TPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREVH 606
                    R + + D LCEAGRFGQKTG+G+Y+Y+    R  +PDPW+   ++      
Sbjct: 547 ---------RTAVIADALCEAGRFGQKTGEGFYRYEAG-SRRPEPDPWVEALIAGKARER 596

Query: 607 HIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFYA 666
            IE+R I+ EEI+ER LY +INE  RILEEG+AARP  IDV ++ GYG+P  KGGPMF+A
Sbjct: 597 GIERRPIAAEEIVERTLYPMINEGARILEEGIAARPSDIDVAWVDGYGFPVGKGGPMFWA 656

Query: 667 ASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQG 704
             VGL T++E+L  ++ +         +  LRRL A G
Sbjct: 657 DHVGLATIVERLDDWHGKT-GRELFAAAPLLRRLAADG 693


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: 1149
Number of extensions: 49
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: 722
Length of database: 707
Length adjustment: 39
Effective length of query: 683
Effective length of database: 668
Effective search space:   456244
Effective search space used:   456244
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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