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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011382757.1 AMB_RS01570 protein meaA
          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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources