GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Magnetospirillum magneticum AMB-1

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_011382757.1 AMB_RS01570 protein meaA

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000009985.1:WP_011382757.1
          Length = 665

 Score =  384 bits (987), Expect = e-111
 Identities = 210/488 (43%), Positives = 306/488 (62%), Gaps = 11/488 (2%)

Query: 83  RGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKV 142
           R + W  R Y+G+++A ESNK Y+  L++GQTGLS+AFDLPTQ GYDSDH LA+GEVGKV
Sbjct: 14  REKPWLFRTYSGHSSAAESNKLYRTNLTKGQTGLSIAFDLPTQTGYDSDHVLAKGEVGKV 73

Query: 143 GVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQND 202
           GV +  L DM  LF+GIPL+K++TSMTIN+ AA LL++YI  AE QG ++  L GT QND
Sbjct: 74  GVPVCHLGDMMTLFEGIPLEKMNTSMTINAPAAWLLSLYIAAAERQGANRSVLNGTTQND 133

Query: 203 ILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFT 262
           ++KEY++RGTYIF PQPS++LT D+I +    VPKWNP+++  YH++EAGA   QE+A+ 
Sbjct: 134 VIKEYLSRGTYIFAPQPSLKLTGDVIAFTYREVPKWNPMNVCSYHLQEAGATPEQELAYA 193

Query: 263 LADGIEYVKAV--IERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWFN 320
           LA  +  +  V       D ++   R+SFF  A   F+ E+ K RA   LW  I    + 
Sbjct: 194 LATAVAVLDTVRPTVPAADFEQVVSRISFFVNAGIRFVTELCKMRAFTELWDEICVGRYG 253

Query: 321 AKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVL---GGTQSLHTNSYDEALS 377
            K+ ++   R+  Q     LT QQPENN+ R+ ++ LA VL      +++   +++EAL 
Sbjct: 254 VKDEKARRFRYGVQVNSLGLTEQQPENNVYRIVMEMLAVVLSKNARARAVQLPAWNEALG 313

Query: 378 LPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGM 437
           LP     + +LR QQI+AYE+ +++  D   G++ I    + + E A + + +I  MGG 
Sbjct: 314 LPRPWDQQWSLRLQQIMAYETDLLEFGDIFDGSHEITRKVEALKEGAREELARIDAMGGA 373

Query: 438 MRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPI-----EVEILKVDPSIR 492
           + A+E  Y+++++ E+  +    IE G++I+VGVN +   EP      E  I+ VDP   
Sbjct: 374 VSAVESSYMKQKLVESNARRIGAIETGEQIVVGVNKWTETEPSPLTTGEGSIMTVDPKAE 433

Query: 493 EKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLRE 552
            +QIERLK  R+ RD K V +AL +LR+AA +    + P I  AH  + T  E    LR+
Sbjct: 434 AEQIERLKAFRAARDAKAVDKALAELRSAANEGRNVMEPSIAAAHAGVTT-GEWAQCLRD 492

Query: 553 IWGEYRAP 560
           ++GEYRAP
Sbjct: 493 VFGEYRAP 500


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: 36
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: 665
Length adjustment: 37
Effective length of query: 526
Effective length of database: 628
Effective search space:   330328
Effective search space used:   330328
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