Aligments for a candidate for mcmA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Acidovorax sp. GW101-3H11

Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Ac3H11_2278 Methylmalonyl-CoA mutase (EC 5.4.99.2)

Query= reanno::PS:Dsui_0519
         (721 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2278
          Length = 722

 Score = 1182 bits (3057), Expect = 0.0
 Identities = 579/705 (82%), Positives = 645/705 (91%)

Query: 15  NLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYADTLPGFAPYLRGPQ 74
           +L+AWAKAAAKSAPGGDV+ALNW+TP+G+TVKPLYT +D   LPYA+TLPGF PYLRGPQ
Sbjct: 16  SLEAWAKAAAKSAPGGDVSALNWVTPDGITVKPLYTAEDTASLPYANTLPGFEPYLRGPQ 75

Query: 75  ATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDNPRVLGD 134
           ATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSD+PRV GD
Sbjct: 76  ATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDHPRVTGD 135

Query: 135 VGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAEEQGVSQEQLSGT 194
           VGKAGVAIDSVEDMKILFD IPLDK+SVSMTMNGAVLP+LAGY+VAAEEQGVSQ++LSGT
Sbjct: 136 VGKAGVAIDSVEDMKILFDQIPLDKVSVSMTMNGAVLPVLAGYVVAAEEQGVSQDKLSGT 195

Query: 195 IQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISISGYHIQEAGANQAIE 254
           IQNDILKEFMVRNTYIYPPKPSM+II DI GYTA++MPKFNSISISGYH+QEAGANQA+E
Sbjct: 196 IQNDILKEFMVRNTYIYPPKPSMRIIGDIIGYTAKNMPKFNSISISGYHMQEAGANQALE 255

Query: 255 LAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKMRAGRMLWHRIMSQF 314
           LAFTLADG EYV+T +ASGLDVD FAGRLSFFWA+GMNFYLE+AKMRA R+LW RIM + 
Sbjct: 256 LAFTLADGKEYVKTAMASGLDVDEFAGRLSFFWAIGMNFYLEVAKMRAARLLWCRIMKET 315

Query: 315 NPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALP 374
             K+ KSLMLRTH QTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALP
Sbjct: 316 GAKNPKSLMLRTHCQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALP 375

Query: 375 TEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWSIIQEIEAMGGMTK 434
           TEFSARIARNTQLIIQEETHI NV+DPWAGSYMMEKLTQDM D AW II+E+EAMGGMT+
Sbjct: 376 TEFSARIARNTQLIIQEETHITNVIDPWAGSYMMEKLTQDMMDAAWKIIEEVEAMGGMTQ 435

Query: 435 AVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDILDIDNHAVREAQIAR 494
           AV+SGWAK+++E  AA+KQARIDSGKDVIVGVNKYKLAKED +DIL IDN  VR+ QIAR
Sbjct: 436 AVDSGWAKLKIEAAAAEKQARIDSGKDVIVGVNKYKLAKEDPVDILQIDNMKVRDGQIAR 495

Query: 495 LKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVGEVSDALEKVFGRFR 554
           L+KIRA+RD+A VQAALDALT  AESGEGNLL+LS+ A+RLRATVGEVSDALEKVFGR R
Sbjct: 496 LEKIRATRDAAKVQAALDALTAAAESGEGNLLELSINAVRLRATVGEVSDALEKVFGRHR 555

Query: 555 ANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLGQDGHDRGAKVVATA 614
           A+ Q ++GVY    +  E W+ +K +I  FAEE+GRRPR+MIAKLGQDGHDRGAKVVATA
Sbjct: 556 ADTQKVTGVYAAAYDSAEGWDKLKTEINAFAEEQGRRPRVMIAKLGQDGHDRGAKVVATA 615

Query: 615 FADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLPALVNSLKEQGADDI 674
           FADLGFD+DMGPLFQTPEE ARQA+ENDVHA+GVS+LAAGHKTL+PA++ SL++QGADDI
Sbjct: 616 FADLGFDVDMGPLFQTPEECARQAIENDVHAVGVSTLAAGHKTLVPAIIQSLRDQGADDI 675

Query: 675 IVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKS 719
           IVF GGVIPAQDYD LY +G K ++GPGT I  SAK VLE+IRK+
Sbjct: 676 IVFVGGVIPAQDYDFLYESGVKGVYGPGTPIPASAKDVLEQIRKA 720


Lambda     K      H
   0.317    0.132    0.380 

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: 1568
Number of extensions: 50
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: 721
Length of database: 722
Length adjustment: 40
Effective length of query: 681
Effective length of database: 682
Effective search space:   464442
Effective search space used:   464442
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 (21.6 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)
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 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