GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Paraburkholderia bryophila 376MFSha3.1

Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate H281DRAFT_02833 H281DRAFT_02833 Cytochrome c, mono- and diheme variants

Query= SwissProt::O34215
         (441 letters)



>FitnessBrowser__Burk376:H281DRAFT_02833
          Length = 438

 Score =  316 bits (810), Expect = 8e-91
 Identities = 182/421 (43%), Positives = 245/421 (58%), Gaps = 28/421 (6%)

Query: 17  ALADDQANDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATP-IGTIYSTNITPDKT 75
           A A D  + AL+KRGEYLA AGDC+ACH+   G+PFAGGLP+  P +GTIYS+NITPD  
Sbjct: 29  AKAVDGNDAALIKRGEYLATAGDCMACHTTAKGKPFAGGLPLKVPMLGTIYSSNITPDPQ 88

Query: 76  TGIGDYSYDDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQA 135
           TGIG +S +DF +A+R GV+K+G  LYPAMPY SYA VSD D+KALYAYF +GV PV QA
Sbjct: 89  TGIGTWSLEDFDRALRKGVSKDGHNLYPAMPYVSYAKVSDGDVKALYAYFRYGVVPVQQA 148

Query: 136 NKDSDIPWPLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPR 195
            + SDI WPL+MRWPL +W  +F      +Q   Q+     RG YLV+GL HC  CHTPR
Sbjct: 149 TRASDIAWPLNMRWPLTVWNWMFLKS-GPYQAKPQQSAEWNRGAYLVQGLAHCSTCHTPR 207

Query: 196 SITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRNDH 255
              MQE+AL   G+  +L GS   +  W   N+      G+G WS   L Q+L+ G    
Sbjct: 208 GFAMQEQALDETGS-GFLGGS--VLADWDGYNITSSPDSGIGGWSHTQLVQYLQTGSVPG 264

Query: 256 TA-AFGGMTDVVEHSLQHLSDDDITAIARYLKSL------GAKDASQTVF-----TQDDQ 303
            A A G M + VEHS   +SD DI AIA Y++++      GA+  S++       + D  
Sbjct: 265 LAQAAGPMAEAVEHSFSKMSDADIGAIATYVRTVPPVNDGGAQSGSRSRSAWGKPSTDVA 324

Query: 304 VAKALWKGDDSQTGASVYVDSCAACHKTDGSRLSALLPGAAWQP----GGAGEPDPTSLI 359
             + +   D +   A +Y+ +CA CH+  G       P   + P       G  +P +L+
Sbjct: 325 RLRGVAMNDGTLDPARLYLGNCATCHQASGKG----TPDGYYPPLLHNSTVGASNPGNLM 380

Query: 360 HIVLTGGTLPGVQGAPTAITMPAFGWRLNDQQVADVVNFIRGSWGNGAKATVTAKDVASL 419
            ++L G      + A   + MPAF  +LND Q+A + N++   +GN A   V+ KDVA L
Sbjct: 381 QVILHGVQR---KAAGNDVGMPAFAAQLNDAQIAALTNYVTTQFGNPAAQRVSEKDVARL 437

Query: 420 R 420
           R
Sbjct: 438 R 438


Lambda     K      H
   0.317    0.133    0.409 

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: 625
Number of extensions: 40
Number of successful extensions: 9
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: 441
Length of database: 438
Length adjustment: 32
Effective length of query: 409
Effective length of database: 406
Effective search space:   166054
Effective search space used:   166054
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: 51 (24.3 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