GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Pseudomonas putida KT2440

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 PP_2479 PP_2479 Cytochrome c family protein

Query= SwissProt::O34215
         (441 letters)



>FitnessBrowser__Putida:PP_2479
          Length = 407

 Score =  244 bits (624), Expect = 3e-69
 Identities = 155/418 (37%), Positives = 239/418 (57%), Gaps = 27/418 (6%)

Query: 2   MKSILALVLGTLSFAALADDQ-ANDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMAT 60
           M  +++ VL   S A LA    A + L+ +GEYL RA +CVACH+V GGQPFAGG+    
Sbjct: 1   MMKLISNVLTLASAALLAQAAYAQEDLLAKGEYLTRAANCVACHTVPGGQPFAGGVEFKL 60

Query: 61  PIGTIYSTNITPDKTTGIGDYSYDDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKA 120
           P G+++S NITPD  TGIG ++ D+F  A++ G+ ++G   YPA PY SY+ +S +D+ A
Sbjct: 61  PFGSLFSPNITPDPQTGIGAWTDDEFVSALQTGIGRDGKHYYPAFPYTSYSKMSRDDILA 120

Query: 121 LYAYFMHGVAPVAQANKDSDIPWPLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRY 180
           +  Y +  + PV QA +++ I +P + RW +  W  +F  D + FQ  +Q      RG+Y
Sbjct: 121 IKGY-LDSLQPVEQAPRENHIGFPFNQRWGMVFWNLLFLND-EPFQADSQRSAEWNRGKY 178

Query: 181 LVEGLGHCGACHTPRSITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWS 240
           LVEG GHCG CH+PR++    +A+S++ +   L+G+   I GW A N+  D   G+G W 
Sbjct: 179 LVEGPGHCGECHSPRNLF---QAVSSERS---LAGNL--IQGWNAYNISADPVHGIGAWP 230

Query: 241 EDDLRQFLRYGRNDHTA-AFGGMTDVVEHSLQHLSDDDITAIARYLKSLGAKDASQTVFT 299
            D L  +L+ G       + G M +VVE+SL+HL+D D  AIA +LK    +        
Sbjct: 231 TDVLAGYLKDGAAPGLGLSSGPMAEVVENSLRHLTDADRQAIAVFLKDSPPRSEG---VP 287

Query: 300 QDDQVAKALWKGDDSQTGASVYVDSCAACHKTDGS---RLSALLPGAAWQPGGAGEPDPT 356
           +  QV  A   G  S  G  ++ ++CA+CH+ DG+     +A+L G         +P  +
Sbjct: 288 RPQQVTLA-EPGSGSALGNKLFAEACASCHRWDGTGNQSQTAMLLGLK----TVNDPAAS 342

Query: 357 SLIHIVLTGGTLPGVQGAPTAITMPAFGWRLNDQQVADVVNFIRGSWG-NGAKATVTA 413
           +L+ I+L+G    G   AP    MP+FG    DQ++A + +F+   +G +GA+ +V A
Sbjct: 343 NLLGILLSG---HGAADAPVNRRMPSFGNIYTDQELAALSSFMLQRFGESGAQVSVPA 397


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: 527
Number of extensions: 45
Number of successful extensions: 8
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: 407
Length adjustment: 32
Effective length of query: 409
Effective length of database: 375
Effective search space:   153375
Effective search space used:   153375
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