GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Haloterrigena daqingensis JX313

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

Query= BRENDA::P22033
         (750 letters)



>NCBI__GCF_001971705.1:WP_076578503.1
          Length = 566

 Score =  463 bits (1191), Expect = e-134
 Identities = 242/550 (44%), Positives = 352/550 (64%), Gaps = 25/550 (4%)

Query: 53  GKNPEDLIWHTPEGISIKPLYSKRDTMDLP--EEL--PGVKPFTRGPYPTMYTFRPWTIR 108
           G+  ED    T   I +  LY+  D  DL   E+L  PG +P+TRGPYPTMY  R WT+R
Sbjct: 30  GERQEDFA--TVSNIDVDRLYTPEDVADLDYLEDLGFPGEEPYTRGPYPTMYRGRTWTMR 87

Query: 109 QYAGFSTVEESNKFYKDNIKAGQQGLSVAFDLATHRGYDSDNPRVRGDVGMAGVAIDTVE 168
           Q+AGF T EE+N+ +   I  GQ GLSVAFD+ T  G DSD+    G++G  GVA+DT+ 
Sbjct: 88  QFAGFGTAEETNERFHYLIDEGQTGLSVAFDMPTLMGLDSDDRMSEGEIGKEGVAVDTLR 147

Query: 169 DTKILFDGIPLEKMSVSMTMNGAVIPVLANFIVTGEEQGVPKEKLTGTIQNDILKEFMVR 228
           D +ILFDGI LE++S S T+N +   + A ++   ++QGVP+E + GT+QND+ KEF+ +
Sbjct: 148 DMEILFDGIDLEEISTSFTINPSAPVIYAMYVAMADQQGVPRENIRGTLQNDMFKEFIAQ 207

Query: 229 NTYIFPPEPSMKIIADIFEYTAKHMPKFNSISISGYHMQEAGADAILELAYTLADGLEYS 288
             ++ PPEPS+ ++ D+ E++ +  P+F+ IS+SGYH++EAG+ A+ ELA+TLADG  Y 
Sbjct: 208 KEWVVPPEPSLDLVTDVLEFSTEETPQFHPISVSGYHIREAGSTAVQELAFTLADGFAYV 267

Query: 289 RTGLQAGLTIDEFAPRLSFFWGIGMNFYMEIAKMRAGRRLWAHLIEKMFQPKNSKSLLLR 348
              ++ GL +DEFAPRLSFF+    +F+ EIAK RA RR++A ++++ +  +  +S  L+
Sbjct: 268 EDAMERGLAVDEFAPRLSFFFNCHNSFFEEIAKYRAARRIYARVMDEWYDAQRDESKRLK 327

Query: 349 AHCQTSGWSLTEQDPYNNIVRTAIEAMAAVFGGTQSLHTNSFDEALGLPTVKSARIARNT 408
            H QT+G SLT Q P NN+VR  I+A+A V GGTQSLHTNSFDEAL LP+  + R+A  T
Sbjct: 328 FHTQTAGQSLTAQQPMNNVVRVTIQALAGVLGGTQSLHTNSFDEALALPSEDAVRVALRT 387

Query: 409 QIIIQEESGIPKVADPWGGSYMMECLTNDVYDAALKLINEIEEMG------GMAKAVAEG 462
           Q II EESG   + DP GGS+ +E LT++  +  ++ + EI EMG      G+ K + +G
Sbjct: 388 QQIIAEESGAADIVDPMGGSFAVEALTDETEERTMRYLTEIREMGEGSMRDGVLKGIDDG 447

Query: 463 IPKLRIEECAARRQARIDSGSEVIVGVNKYQLEKEDAVEVLAIDNTSVRNRQIEKLKKIK 522
                I++ +   Q R++ G EV+VGVN++ LE++ + E L ID T+   RQ+E+L+++K
Sbjct: 448 YFLREIQDASYEYQERVERGEEVVVGVNEFTLEEDTSPETLKIDETTA-ERQLERLEQVK 506

Query: 523 SSRDQALAERCLAALTECAASGDGNILALAVDASRARCTVGEITDALKKVFGEHKANDRM 582
           + RD A  E  L  L      G+ N + + V+A +A  TVGEI    +    EH      
Sbjct: 507 AQRDDAAVEDALEELQRTIDRGE-NTIPVLVEAVKAYATVGEIMQVFE---DEH------ 556

Query: 583 VSGAYRQEFG 592
             GAY +E G
Sbjct: 557 --GAYSEEIG 564


Lambda     K      H
   0.318    0.135    0.391 

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: 961
Number of extensions: 43
Number of successful extensions: 3
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: 750
Length of database: 566
Length adjustment: 38
Effective length of query: 712
Effective length of database: 528
Effective search space:   375936
Effective search space used:   375936
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: 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