GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Sphingobium czechense LL01

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_066599254.1 V473_RS00615 hypothetical protein

Query= BRENDA::P07896
         (722 letters)



>NCBI__GCF_001046645.1:WP_066599254.1
          Length = 689

 Score =  478 bits (1231), Expect = e-139
 Identities = 277/680 (40%), Positives = 399/680 (58%), Gaps = 34/680 (5%)

Query: 10  SLAMIRLCNPPVNA--VSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFS 67
           S+ ++R  N PVNA  V   +++ +   + +A +D  V AI++ G    F AGADI  F 
Sbjct: 10  SVLVVRFDNSPVNALTVGGGLVQAIERRVAQAQTDERVDAIILTGGGTVFSAGADIADFE 69

Query: 68  AFTPGL-ALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTL 126
                + A+ SL+  I+  +KPV+AAI+G+ LGGGLELAL  H+R+A++ A+ G PE++L
Sbjct: 70  GAPERIDAIRSLMQSIENCRKPVVAAIEGLCLGGGLELALAAHFRVASSTAKFGFPEISL 129

Query: 127 GILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKF-AQ 185
           G+LPG  GTQ  PR+ G   A+DL+ SGK +SA +AL +G++D + + D VE A+   A 
Sbjct: 130 GLLPGGGGTQRSPRLAGAGNAIDLMLSGKSVSAAKALEIGLIDRIAEGDVVEAALAMLAA 189

Query: 186 KIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYE 245
            ++      RR  + PVP   ++D+    A  +      G  A   CVR+I  +     +
Sbjct: 190 GLVGST---RRSGSLPVPQ--DLDAAIDSAERRTGLTDAG-RAIIACVRAIAQT---DLQ 240

Query: 246 VGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLG 305
            G+K E + F  L  S Q++AL++AFF  +   K   P G       ++ V  V V+G G
Sbjct: 241 AGLKLEAEQFGALMTSEQSRALRHAFFGRRIVGK--IPGGVR---VESKGVRHVTVVGGG 295

Query: 306 TMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKP--KLR 363
            MG GIAIS     + V  VE+ P+  D  +  I  +L ++A +A      + +    L 
Sbjct: 296 LMGTGIAISLLNADLGVTVVEAKPEGFDKCRASIEASLRRDADKARITAATADRRIGALN 355

Query: 364 FSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDR 423
              S  E    DL +EAVFEDM+ K++VF  L  +   GA L +NTS L++D IA  T R
Sbjct: 356 MGRSIDEAMPSDLYIEAVFEDMDAKREVFQALDRIAPLGAILASNTSTLDLDAIAQFTSR 415

Query: 424 PQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRM 483
           P+ V+G HFFSPA++MRLLEV+    +SP T+A+ M+ +K IGK GVV G C GF+GNR+
Sbjct: 416 PEAVVGLHFFSPANIMRLLEVVRGARTSPETLASAMAFAKSIGKTGVVAGVCDGFIGNRI 475

Query: 484 LAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSL 543
              Y  Q +FLLEEG+ P  +D  LE FG  MGP RV DLAG D+GW IRK + +  P  
Sbjct: 476 FEEYLRQAWFLLEEGALPHQIDAALEAFGMAMGPCRVMDLAGQDIGWNIRKRRAVEQPDR 535

Query: 544 PPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYR 603
           P            YS + D++CE GRFGQKTG G+Y Y  P GR  + DP +   +  + 
Sbjct: 536 P------------YSKIPDLVCELGRFGQKTGTGFYLY--PDGRTPQRDPLIEALIVSHS 581

Query: 604 EVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPM 663
                ++R I   EI+ERC++++INE  +++ EG+A RP  +D+IYL GYG+P  +GGPM
Sbjct: 582 RQIDFDRRVIDDSEIVERCIFAMINEGAKLVGEGIAYRPVDVDIIYLDGYGFPASRGGPM 641

Query: 664 FYAASVGLPTVLEKLQKYYR 683
           F+A  VGLP +LEK+ +Y R
Sbjct: 642 FHADQVGLPHLLEKMAQYAR 661


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: 1084
Number of extensions: 43
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: 689
Length adjustment: 39
Effective length of query: 683
Effective length of database: 650
Effective search space:   443950
Effective search space used:   443950
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 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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