GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Haloterrigena daqingensis JX313

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_076578503.1 BB347_RS03070 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_001971705.1:WP_076578503.1
          Length = 566

 Score =  625 bits (1612), Expect = 0.0
 Identities = 298/560 (53%), Positives = 424/560 (75%), Gaps = 8/560 (1%)

Query: 4   FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYME 63
           +D E L+ I+E  ++WE  T+   LE+  ER+E F T    ++ R+YTP D+  D +Y+E
Sbjct: 2   YDDEDLEAIRESGEKWETDTLDPVLERHGERQEDFATVSNIDVDRLYTPEDVA-DLDYLE 60

Query: 64  KLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLP 123
            LGFPGE P+TRG Y TMYRGR WTMRQ+AG+ TAEE+N+R+ YL+ +GQTGLSVAFD+P
Sbjct: 61  DLGFPGEEPYTRGPYPTMYRGRTWTMRQFAGFGTAEETNERFHYLIDEGQTGLSVAFDMP 120

Query: 124 TQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYIL 183
           T +G DSD  ++EGE+GK GVA+D+L DM ILFDGI L+++STS TIN +A  + AMY+ 
Sbjct: 121 TLMGLDSDDRMSEGEIGKEGVAVDTLRDMEILFDGIDLEEISTSFTINPSAPVIYAMYVA 180

Query: 184 VAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISI 243
           +A++QGV +E +RGT+QND+ KE+IA+  ++ PP+PS+ L TD++ +  E  P+++PIS+
Sbjct: 181 MADQQGVPRENIRGTLQNDMFKEFIAQKEWVVPPEPSLDLVTDVLEFSTEETPQFHPISV 240

Query: 244 SGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAK 303
           SGYHIREAG+ AVQE+AFTLADG  YV+  +ERG+ VD+FAPRLSFFF  HN+F EEIAK
Sbjct: 241 SGYHIREAGSTAVQELAFTLADGFAYVEDAMERGLAVDEFAPRLSFFFNCHNSFFEEIAK 300

Query: 304 FRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGG 363
           +RAARR++A +M EW++A+   S  L+FHTQTAG +LTAQQP NN+VRV IQALA VLGG
Sbjct: 301 YRAARRIYARVMDEWYDAQRDESKRLKFHTQTAGQSLTAQQPMNNVVRVTIQALAGVLGG 360

Query: 364 TQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEE 423
           TQSLHTNS+DEAL+LP+E +VR+ALRTQQIIA ESG  D VDP+GG++ +E LTD   E 
Sbjct: 361 TQSLHTNSFDEALALPSEDAVRVALRTQQIIAEESGAADIVDPMGGSFAVEALTDETEER 420

Query: 424 ALKYIEKIQKMG------GMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTD 477
            ++Y+ +I++MG      G+++ I+ GY  +EI +A+Y+YQ+ +E G+ ++VGVN F  +
Sbjct: 421 TMRYLTEIREMGEGSMRDGVLKGIDDGYFLREIQDASYEYQERVERGEEVVVGVNEFTLE 480

Query: 478 EPIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAH 537
           E    E LK+D +  E+Q+ERL++++++RD+  V++AL++L+   ++  EN +P ++EA 
Sbjct: 481 EDTSPETLKIDETTAERQLERLEQVKAQRDDAAVEDALEELQRTIDR-GENTIPVLVEAV 539

Query: 538 RHLATLQEVTDVLREIWGEY 557
           +  AT+ E+  V  +  G Y
Sbjct: 540 KAYATVGEIMQVFEDEHGAY 559


Lambda     K      H
   0.318    0.134    0.388 

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: 846
Number of extensions: 33
Number of successful extensions: 4
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: 563
Length of database: 566
Length adjustment: 36
Effective length of query: 527
Effective length of database: 530
Effective search space:   279310
Effective search space used:   279310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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