GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Pedobacter sp. GW460-11-11-14-LB5

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate CA265_RS25460 CA265_RS25460 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>FitnessBrowser__Pedo557:CA265_RS25460
          Length = 515

 Score =  641 bits (1654), Expect = 0.0
 Identities = 328/523 (62%), Positives = 406/523 (77%), Gaps = 10/523 (1%)

Query: 35  KEKFMTDDGFEIKRIYTPADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAG 94
           ++K  T  G EIK +YT A        ME+L  PGE+PFTRG+   MYRGR+WTMRQYAG
Sbjct: 3   EKKHTTTSGIEIKALYTKA------KPMEEL--PGEFPFTRGIQKDMYRGRLWTMRQYAG 54

Query: 95  YATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRI 154
           ++TAEESNKRY YLL+QG TGLSVAFDLPTQ+GYDSDH +A+GEVGKVGVAIDSL D+ I
Sbjct: 55  FSTAEESNKRYHYLLAQGTTGLSVAFDLPTQIGYDSDHEMADGEVGKVGVAIDSLKDIEI 114

Query: 155 LFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQNDILKEYIARGTYI 214
           LFDGI L  ++TSMTIN+TA+ LLAMYI +A++QG   +++ GT+QNDILKEY ARGTYI
Sbjct: 115 LFDGIQLKDITTSMTINATASILLAMYIALAKKQGADLKQISGTIQNDILKEYAARGTYI 174

Query: 215 FPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVI 274
           +PP+ SMRL TDI  +C++ VPKWN ISISGYHIREAG+ AVQE+AFTLA+G  Y+KA +
Sbjct: 175 YPPKQSMRLITDIFEFCSKEVPKWNTISISGYHIREAGSTAVQELAFTLANGKTYLKAAL 234

Query: 275 ERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQ 334
           ++G+D++ FA RLSFFF  HNNF EEIAKFRAARR+WA I K+   A + ++ MLRFHTQ
Sbjct: 235 DKGLDINVFAKRLSFFFNCHNNFFEEIAKFRAARRMWAKITKD-LGATDEKAQMLRFHTQ 293

Query: 335 TAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQII 394
           T GSTLTAQQP NN++RV+ QA+AAVLGGTQSLHTN YDEALSLPTE + +IALRTQQII
Sbjct: 294 TGGSTLTAQQPLNNVIRVSNQAMAAVLGGTQSLHTNGYDEALSLPTESAAKIALRTQQII 353

Query: 395 AYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAA 454
           A+ESGV DTVDPL G++++E LTD +   A  YI++I  MGG + AIE  Y+Q EIA A+
Sbjct: 354 AFESGVTDTVDPLAGSFFVENLTDEVETAAWAYIDRIDAMGGSVNAIESDYMQNEIAGAS 413

Query: 455 YKYQKEIEEGKRIIVGVNAFVTDEPIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEA 514
           Y+YQKEIE G+RI VGVN F  +E    E+  +D SIR+ Q E+L+ L++ RDN  V++A
Sbjct: 414 YQYQKEIESGERISVGVNKFTQEEEGLTEVFNIDDSIRKLQSEKLEILKTTRDNDAVEKA 473

Query: 515 LDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEY 557
           L  L  AA K + NLMP II+A    ATL E+ DV R  +G Y
Sbjct: 474 LQSLHEAA-KGETNLMPLIIDAVEKYATLGEIADVFRGTFGVY 515


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: 798
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: 515
Length adjustment: 35
Effective length of query: 528
Effective length of database: 480
Effective search space:   253440
Effective search space used:   253440
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: 52 (24.6 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