Aligments for a candidate for mcmA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Phaeobacter inhibens BS107

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate GFF2118 PGA1_c21510 methylmalonyl-CoA mutase BhbA

Query= SwissProt::Q3J4D7
         (709 letters)



>FitnessBrowser__Phaeo:GFF2118
          Length = 707

 Score = 1170 bits (3026), Expect = 0.0
 Identities = 590/707 (83%), Positives = 641/707 (90%)

Query: 1   MTEDLDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTR 60
           MT   D WR LAEKEL+G+  D+LTWNTLEGI VKPLYT AD   + H+  +PG  PFTR
Sbjct: 1   MTTKTDDWRALAEKELRGRPLDALTWNTLEGIDVKPLYTEADTKDLPHMGTMPGFGPFTR 60

Query: 61  GVRATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120
           GV+ATMYAGRPWTIRQYAGFSTAE SNAFYR+ LAAGQQGVSVAFDLATHRGYDSDHPRV
Sbjct: 61  GVKATMYAGRPWTIRQYAGFSTAEESNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRV 120

Query: 121 VGDVGKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAAL 180
           +GDVGKAGVAIDS+EDMKILF+GIPL+++SVSMTMNGAVIPILA+FIV GEEQG  ++ L
Sbjct: 121 MGDVGKAGVAIDSVEDMKILFDGIPLDQVSVSMTMNGAVIPILASFIVAGEEQGHDKSLL 180

Query: 181 SGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANL 240
           +GTIQNDILKEFMVRNTYIYPPEPSMRII+DIIEYTS EMPKFNSISISGYHMQEAGANL
Sbjct: 181 AGTIQNDILKEFMVRNTYIYPPEPSMRIISDIIEYTSNEMPKFNSISISGYHMQEAGANL 240

Query: 241 VQELAYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIM 300
           VQELAYTLADGREYVRAA+  GM+VD FAGRLSFFFAIGMNFFME AKLRAAR LWHR+M
Sbjct: 241 VQELAYTLADGREYVRAAMEAGMDVDKFAGRLSFFFAIGMNFFMEIAKLRAARTLWHRVM 300

Query: 301 SEFAPKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAI 360
           ++F  K   S MLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSA LGGTQSLHTNALDEAI
Sbjct: 301 TDFDAKNDRSKMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAVLGGTQSLHTNALDEAI 360

Query: 361 ALPTEFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGG 420
           ALPT+FSARIARNTQ++LQEETGVT VVDPLAGSYYVESLT EL EKAWAL+EEVE MGG
Sbjct: 361 ALPTDFSARIARNTQLVLQEETGVTNVVDPLAGSYYVESLTNELIEKAWALMEEVEEMGG 420

Query: 421 MTKAVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQ 480
           MTKAVASGMPKLRIEESAARRQA IDRGE+VIVGVNKYR  KEDPI+ILD+DNVAVRD+Q
Sbjct: 421 MTKAVASGMPKLRIEESAARRQAMIDRGEEVIVGVNKYRKEKEDPIDILDVDNVAVRDSQ 480

Query: 481 IARLEKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGR 540
           IARLE +RA RD AAC+AALD LTR A EGGNLL AAV+A+RARASVGEISMAMEK FGR
Sbjct: 481 IARLETLRADRDSAACEAALDNLTRVAKEGGNLLAAAVEAARARASVGEISMAMEKEFGR 540

Query: 541 HRAEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIA 600
           H AEVKTL+GVYGAAYEGD+GFA IQ+ +E FAE EGRRPR+LVVKMGQDGHDRGAKVIA
Sbjct: 541 HSAEVKTLAGVYGAAYEGDEGFAAIQKSIEDFAEAEGRRPRLLVVKMGQDGHDRGAKVIA 600

Query: 601 TAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAG 660
           TAFADIGFDVDVG LFQTP+EAAQDAIDNDVHVVGISS AAGHKTLAP+L++ALKE+GA 
Sbjct: 601 TAFADIGFDVDVGPLFQTPDEAAQDAIDNDVHVVGISSQAAGHKTLAPQLVKALKEQGAE 660

Query: 661 EILVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREA 707
           +I+VICGGVIPQQDY FL   GVKAIFGPGTNIP AA+ IL LIR++
Sbjct: 661 DIIVICGGVIPQQDYQFLYDNGVKAIFGPGTNIPEAAQDILKLIRQS 707


Lambda     K      H
   0.318    0.133    0.377 

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: 1448
Number of extensions: 36
Number of successful extensions: 1
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: 709
Length of database: 707
Length adjustment: 39
Effective length of query: 670
Effective length of database: 668
Effective search space:   447560
Effective search space used:   447560
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