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.
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:
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