GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Rhodobacter ovatus JA234

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_097029881.1 CRO07_RS06500 protein meaA

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_900207575.1:WP_097029881.1
          Length = 652

 Score =  363 bits (931), Expect = e-104
 Identities = 210/484 (43%), Positives = 289/484 (59%), Gaps = 13/484 (2%)

Query: 87  WTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKVGVAI 146
           W  R YAG++TA  SN  Y+  L++GQTGLSVAFDLPTQ GYDSDH LA GEVGKVGV +
Sbjct: 8   WLFRTYAGHSTARASNALYRTNLAKGQTGLSVAFDLPTQTGYDSDHELARGEVGKVGVPV 67

Query: 147 DSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQNDILKE 206
             L DMR LFD IPL++++TSMTIN+TA  LLA+YI VAEEQG    KL+GTVQND++KE
Sbjct: 68  CHLGDMRALFDQIPLEQMNTSMTINATAPWLLALYIAVAEEQGADVSKLQGTVQNDLMKE 127

Query: 207 YIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFTLADG 266
           Y++RGTYI PP+PS+R+ TD+  Y   ++PKWNP+++  YH++EAGA   QE+AF LA G
Sbjct: 128 YLSRGTYICPPRPSLRMITDVAAYTQTHLPKWNPMNVCSYHLQEAGATPEQELAFALATG 187

Query: 267 IEYVKAVIER--GMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWFNAKNP 324
           I  +  +  +    D      R+SFF  A   F+ E+ K RA   LW  I ++ +     
Sbjct: 188 IAVLDDLRAKVPAADFPAMVGRISFFVNAGIRFVTELCKMRAFVDLWDEICRDRYGITEE 247

Query: 325 RSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVL---GGTQSLHTNSYDEALSLPTE 381
           +    R+  Q     LT QQPENN+ R+ I+ LA  L      +++   +++EAL LP  
Sbjct: 248 KYRRFRYGVQVNSLGLTEQQPENNVYRILIEMLAVTLSKKARARAVQLPAWNEALGLPRP 307

Query: 382 KSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAI 441
              + +LR QQI+AYES +++  D   G   I+   + +   A + +  I  MGG + AI
Sbjct: 308 WDQQWSLRMQQILAYESDLLEYDDLFDGNPAIDRKVEALKAGAREELTHIDAMGGAIDAI 367

Query: 442 ERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEV-----EILKVDPSIREKQI 496
           +  Y++  + EA  +    +E G+ ++VGVN + T  P  +      I+  DP     QI
Sbjct: 368 D--YMKARLVEANAERIARVESGETVVVGVNRWTTGAPSPLTTGDGAIMVADPEAERDQI 425

Query: 497 ERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGE 556
           ERL   R+ RD   V  AL +LR AA    EN+MP  I A +  AT  E    LR  +GE
Sbjct: 426 ERLNAWRATRDAAAVSAALAELRRAA-TSGENVMPASIAAAKAGATTGEWAAELRRAFGE 484

Query: 557 YRAP 560
           +R P
Sbjct: 485 FRGP 488


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: 779
Number of extensions: 36
Number of successful extensions: 6
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: 652
Length adjustment: 37
Effective length of query: 526
Effective length of database: 615
Effective search space:   323490
Effective search space used:   323490
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