GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Pedo557:CA265_RS25460 CA265_RS25460
           methylmalonyl-CoA mutase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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