Aligments for a candidate for mcmA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Klebsiella michiganensis M5al

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate BWI76_RS23935 BWI76_RS23935 methylmalonyl-CoA mutase

Query= SwissProt::P27253
         (714 letters)



>FitnessBrowser__Koxy:BWI76_RS23935
          Length = 714

 Score = 1318 bits (3412), Expect = 0.0
 Identities = 666/714 (93%), Positives = 687/714 (96%)

Query: 1   MSNVQEWQQLANKELSRREKTVDSLVHQTAEGIAIKPLYTEADLDNLEVTGTLPGLPPYV 60
           MS +QEWQ LANKELSRREKTVD LV QTAEGIA+KPLYTEADLDNLEVTGTLPGLPPYV
Sbjct: 1   MSELQEWQTLANKELSRREKTVDDLVKQTAEGIAVKPLYTEADLDNLEVTGTLPGLPPYV 60

Query: 61  RGPRATMYTAQPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPR 120
           RGPRATMYTAQPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPR
Sbjct: 61  RGPRATMYTAQPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPR 120

Query: 121 VAGDVGKAGVAIDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDK 180
           VAGDVGKAGVAIDTVEDMK+LFD+IPLDKMSVSMTMNGAVLPV+AFYIVAAEEQGV  ++
Sbjct: 121 VAGDVGKAGVAIDTVEDMKILFDRIPLDKMSVSMTMNGAVLPVMAFYIVAAEEQGVASEQ 180

Query: 181 LTGTIQNDILKEYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGAN 240
           LTGTIQNDILKEYLCRNTYIYPPKPSMRIIADIIAWCS  MPRFNTISISGYHMGEAGAN
Sbjct: 181 LTGTIQNDILKEYLCRNTYIYPPKPSMRIIADIIAWCSDYMPRFNTISISGYHMGEAGAN 240

Query: 241 CVQQVAFTLADGIEYIKAAISAGLKIDDFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEA 300
           CVQQVAFTLADGIEYIKAA+ AGLKIDDFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEA
Sbjct: 241 CVQQVAFTLADGIEYIKAALCAGLKIDDFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEA 300

Query: 301 VSGFGAQDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATLGGTQSLHTNAFDEA 360
           VSGFGA +PKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEAL ATLGGTQSLHTNAFDEA
Sbjct: 301 VSGFGATNPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALGATLGGTQSLHTNAFDEA 360

Query: 361 LGLPTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEAG 420
           LGLPTDFSARIARNTQIIIQEESE+CRTVDPLAGSYY+ESLTDQIVKQARAIIQQI EAG
Sbjct: 361 LGLPTDFSARIARNTQIIIQEESEICRTVDPLAGSYYVESLTDQIVKQARAIIQQIAEAG 420

Query: 421 GMAKAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDHEDETDVLEIDNVMVRNE 480
           GMAKAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKL+ EDET VLEIDNV VRNE
Sbjct: 421 GMAKAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLEKEDETAVLEIDNVKVRNE 480

Query: 481 QIASLERIRATRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDALEVAFD 540
           QIASLE+IRA RDD  V AALNALTHAAQH+ENLLAAA+NAARVRATLGEISDALE AFD
Sbjct: 481 QIASLEKIRAQRDDVTVKAALNALTHAAQHHENLLAAAINAARVRATLGEISDALEAAFD 540

Query: 541 RYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGHDRG 600
           RYLVPSQCVTGVIAQSYHQS+ +A EFDAIVAQTE+FL DNGRRPRILIAKMGQDGHDRG
Sbjct: 541 RYLVPSQCVTGVIAQSYHQSDTAAGEFDAIVAQTERFLMDNGRRPRILIAKMGQDGHDRG 600

Query: 601 AKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPELVEALK 660
           AKVIASAYSDLGFDVDLSPMFSTPEEIARLA+ENDVHVVGASSLAAGHKTLIPELV ALK
Sbjct: 601 AKVIASAYSDLGFDVDLSPMFSTPEEIARLAIENDVHVVGASSLAAGHKTLIPELVAALK 660

Query: 661 KWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLDSVRDVLNLISQHHD 714
           KWGREDICV+AGGVIPPQDYAFLQ RGVAAIYGPGTPML+SVRDVL  ISQHHD
Sbjct: 661 KWGREDICVIAGGVIPPQDYAFLQARGVAAIYGPGTPMLESVRDVLTRISQHHD 714


Lambda     K      H
   0.318    0.133    0.381 

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: 1494
Number of extensions: 35
Number of successful extensions: 2
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: 714
Length of database: 714
Length adjustment: 39
Effective length of query: 675
Effective length of database: 675
Effective search space:   455625
Effective search space used:   455625
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: 55 (25.8 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)
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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 paper from 2022 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