Alignments for a candidate for ech in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Marinobacter adhaerens HP15

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF4001 HP15_3941 fatty oxidation complex alpha subunit

Query= BRENDA::P07896
         (722 letters)



>FitnessBrowser__Marino:GFF4001
          Length = 702

 Score =  517 bits (1332), Expect = e-151
 Identities = 295/704 (41%), Positives = 428/704 (60%), Gaps = 33/704 (4%)

Query: 10  SLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAF 69
           ++ +I +  PPVNA+   V   +   L++   D   +A+++      F AGADI  F   
Sbjct: 17  NIGVITVNYPPVNALGQAVRSGLLAALEQGQKDTEARALLLVCEGRTFIAGADIREFGKP 76

Query: 70  TPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGIL 129
                L +LV+  +   KP++AAI G ALGGGLE AL CHYR+A + A+VGLPEV LG+L
Sbjct: 77  MQEPTLPTLVNTFENSDKPLVAAIHGTALGGGLETALSCHYRVAISSAKVGLPEVKLGLL 136

Query: 130 PGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEA-IKFAQKII 188
           PGA GTQ LPR+ G   AL++IT+G+++ A +AL LGILDAV + D +    + +AQK++
Sbjct: 137 PGAGGTQRLPRLTGARKALEMITTGEFVGAKDALALGILDAVEEGDDIRAVGMAYAQKVV 196

Query: 189 D--KPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEV 246
           D  KP+   R     + +    D VF +   +++K+  G+ +P  CV +++A+   P++ 
Sbjct: 197 DEGKPVRRVRDITDKIEADKGSD-VFDQFRDELKKRARGLFSPFKCVDAVEAAFNLPFDE 255

Query: 247 GIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGT 306
           G+K E +LFM    S Q   L ++FF E+  +K    S    K    + V SVG++G GT
Sbjct: 256 GMKRERELFMECMESPQRAGLIHSFFGEREVSKVKGLS----KDTPVRDVKSVGIIGAGT 311

Query: 307 MGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAH------QNGQASAKP 360
           MG GIA++F  VGI V  VE   + LD    II    E  A +        +   A   P
Sbjct: 312 MGGGIAMNFVNVGIPVTIVEVKQEALDKGLAIIRRNYENSAKKGKLTQEQVEQRMALITP 371

Query: 361 KLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASS 420
            L +     +   VDLV+EAVFE+M +KK++FA+L  +CKPGA L +NTS L++D+IAS+
Sbjct: 372 SLTYD----DFRDVDLVIEAVFENMAIKKEIFAKLDEVCKPGAILASNTSTLDIDEIASA 427

Query: 421 TDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVG 480
           T RP+ V+G HFFSPA+VM+LLE +    +S    ATVM+++KKI K+GV+VGNCYGFVG
Sbjct: 428 TKRPEDVVGMHFFSPANVMKLLENVRGSKTSDEVKATVMAVAKKIKKVGVMVGNCYGFVG 487

Query: 481 NRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTG 540
           NRML     +   L++EG+ P+ VD VL + GF MG F +SDLAG+DVG++IR+ +   G
Sbjct: 488 NRMLHKRGTEAMSLVDEGATPQQVDKVLTDLGFPMGQFAMSDLAGIDVGYRIREERRKAG 547

Query: 541 PSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLS 600
             +P             +   D L E GR GQKT  G Y+Y++   R   PDP +   + 
Sbjct: 548 EDIP-------------ASWMDKLAEQGRLGQKTQAGVYKYEEG-SRKPIPDPEVEQLIE 593

Query: 601 QYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKG 660
           Q+R+   I  R I+ +EILERC+Y +INE  +ILEEG+A RP  ID+++++GYG+P ++G
Sbjct: 594 QFRKEQGITPREITNQEILERCVYVMINEGAKILEEGIADRPLDIDIVWIYGYGFPAYRG 653

Query: 661 GPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQG 704
           GPMF+A   GL T+L  ++K Y+      Q EP+  L +LVA+G
Sbjct: 654 GPMFWADQEGLDTILSAVKK-YQDTVGGEQWEPAALLEKLVAEG 696


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: 1185
Number of extensions: 55
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 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