Alignments for a candidate for ech in Brevibacterium jeotgali SJ5-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Brevibacterium jeotgali SJ5-8

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_101589956.1 BJEO58_RS13310 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::P07896
         (722 letters)



>NCBI__GCF_900169175.1:WP_101589956.1
          Length = 702

 Score =  531 bits (1368), Expect = e-155
 Identities = 310/705 (43%), Positives = 422/705 (59%), Gaps = 33/705 (4%)

Query: 5   LRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIH 64
           L +   +A++ L +PPVNA+S  V   +R+    A +D   KAIV+  A   F AGADI 
Sbjct: 10  LEIEEGIAVVTLDSPPVNALSQAVRSGLRDAFAAANADDAAKAIVLICAGRTFIAGADIS 69

Query: 65  GFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEV 124
            F +  P     S+   +    KPV+AAI G ALGGGLE+AL  HYR+A   A+VGLPEV
Sbjct: 70  EFGSDAPKDTGASIFSVLDDSPKPVIAAIHGTALGGGLEVALSTHYRVATTSAKVGLPEV 129

Query: 125 TLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVE-EAIKF 183
            LG+LPG  GTQ LPR+ G   ALDLITSG+++ A EAL LGI+D VV  + +    ++F
Sbjct: 130 HLGLLPGGGGTQRLPRLTGAATALDLITSGRHVPAAEALDLGIIDEVVADEDLRGSTLRF 189

Query: 184 AQKIIDK--PIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVK 241
           A++I+D   P+   R  ++ + +  +   +F   IA   K + G LAP   V  I+A+V 
Sbjct: 190 ARQIVDAGGPLPRVRDLDEKIAADRDDPELFDRFIASHPKLFRGFLAPTEIVACIRAAVT 249

Query: 242 HPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGV 301
            P++ G+ EE++ F  L  S ++ A +Y FFAE++A K +     + +     PVS+VG+
Sbjct: 250 RPFDDGMAEEQERFQTLLTSSESAAQRYYFFAERAARKIADVPADTPRI----PVSTVGI 305

Query: 302 LGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAH-QNGQASAKP 360
           +G GTMG GIA++FA  GI V  VE   + LD     I    E+ AS+      Q   + 
Sbjct: 306 IGAGTMGGGIAMNFATAGIPVTLVEQKQEALDRGLATIRKNYERTASKGRITTAQVEERM 365

Query: 361 KLRFSS-STKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIAS 419
            L   S S  +L+TVD+V+EAVFE M++KK VF +L  +CKPGA L TNTSALNVD+IA+
Sbjct: 366 ALITGSISMDDLATVDMVIEAVFERMDIKKDVFTQLDRICKPGAILATNTSALNVDEIAA 425

Query: 420 STDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFV 479
            T RP+ V+GTHFFSPA+VM+LLE +    +S   IATVM+LS+ IGKI V+VG C GFV
Sbjct: 426 VTSRPEYVVGTHFFSPANVMKLLENVRGEKTSKEVIATVMALSRTIGKIAVLVGVCPGFV 485

Query: 480 GNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLT 539
           GNR+L         L+ EG+ P DVD  L  FG  MG +++SDLAGLD+GW         
Sbjct: 486 GNRILYARSRASEQLVMEGAMPWDVDRALTNFGLPMGTYQMSDLAGLDIGW--------- 536

Query: 540 GPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFL 599
                       +G     P+ D LCE  R GQKTG G+Y YD+   R   P P  +  +
Sbjct: 537 -----------VKGEPTAYPIKDALCEMDRRGQKTGAGFYDYDE--NRTATPSPITAQIV 583

Query: 600 SQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHK 659
              R    +  R IS+EEILER L  ++NE F+IL+EGMA R   IDV+Y++GYGWP ++
Sbjct: 584 EDQRAKAGVTPREISEEEILERTLLPMVNEGFKILQEGMAERASDIDVVYVNGYGWPVYR 643

Query: 660 GGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQG 704
           GGPMFYA  +G  TVLEKL+ Y  +  +     P+  L  +VA+G
Sbjct: 644 GGPMFYAEQLGAETVLEKLRGYAERLGE--DFAPAALLEAVVAKG 686


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: 1100
Number of extensions: 47
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: 702
Length adjustment: 39
Effective length of query: 683
Effective length of database: 663
Effective search space:   452829
Effective search space used:   452829
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 24 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 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