GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Caulobacter crescentus NA1000

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate CCNA_03177 CCNA_03177 methylmalonyl-CoA mutase MeaA-like protein

Query= BRENDA::O74009
         (563 letters)



>FitnessBrowser__Caulo:CCNA_03177
          Length = 662

 Score =  377 bits (969), Expect = e-109
 Identities = 213/486 (43%), Positives = 301/486 (61%), Gaps = 15/486 (3%)

Query: 87  WTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKVGVAI 146
           W  R YAG++TAE+SN  Y+  L++GQTGLSVAFDLPTQ GYD DH LA GEVGKVGV I
Sbjct: 14  WIFRTYAGHSTAEKSNALYRANLAKGQTGLSVAFDLPTQTGYDPDHILARGEVGKVGVPI 73

Query: 147 DSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQNDILKE 206
             L DMR LF  IPL+K++TSMTIN+ AA LLAMY+ +A+EQG  ++ L+GT QND++KE
Sbjct: 74  SHLGDMRQLFSEIPLEKMNTSMTINAPAAWLLAMYVALADEQGADRKLLQGTTQNDLIKE 133

Query: 207 YIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFTLADG 266
           Y++RGTYIFPP PS+RL  D+I +C   VPKWNP+++  YH++EAGA   QE+AF LA  
Sbjct: 134 YLSRGTYIFPPGPSLRLIGDMIAWCYREVPKWNPMNVCSYHLQEAGATPEQELAFALATA 193

Query: 267 IEYVKAVIERGM----DVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWFNAK 322
           I  +  V   G     D +  A R+SFF  A   F+ E+ K R+  +LW  I+ E +  +
Sbjct: 194 ISVLDTVKAGGQVPDEDFEIVASRISFFVNAGVRFVTELCKMRSFTKLWDQILLERYGVQ 253

Query: 323 NPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVL---GGTQSLHTNSYDEALSLP 379
           +P++   R+  Q     LT QQPENN+ R+ I+ALA  L      ++L   +++EAL LP
Sbjct: 254 DPKARRFRYGVQVNSLGLTEQQPENNVYRILIEALAVTLSKDARCRALQLPAWNEALGLP 313

Query: 380 TEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMR 439
                + +LR QQ++AYE+ +++  D   G++ +E     + + AL  +  I +MGG   
Sbjct: 314 RPFDQQWSLRLQQVLAYETDLLEYEDLFDGSHVVEAKVAELSKGALAQLTLIDEMGGAQN 373

Query: 440 AIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDE--PI---EVEILKVDPSIREK 494
           AI+  Y++ E+  +  K  + +E G+  +VGVN +   E  P+   E  I  VDP +   
Sbjct: 374 AID--YMKSELVASNAKRVRAVETGEMTVVGVNRWTETEASPLSAGESAIETVDPRLEAG 431

Query: 495 QIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIW 554
            +ER+K  R  RD   V+ AL  L+ AA +E  N+M   I A +   T  E +  LRE++
Sbjct: 432 VVERIKAWREARDAVAVEAALAALK-AAAREGRNVMEPSIAAAKAGVTTGEWSGALREVF 490

Query: 555 GEYRAP 560
           GEYR P
Sbjct: 491 GEYRGP 496


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: 809
Number of extensions: 42
Number of successful extensions: 5
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: 662
Length adjustment: 37
Effective length of query: 526
Effective length of database: 625
Effective search space:   328750
Effective search space used:   328750
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 17 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