GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-cytc in Paraburkholderia bryophila 376MFSha3.1

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate H281DRAFT_03306 H281DRAFT_03306 Cytochrome c, mono- and diheme variants

Query= reanno::WCS417:GFF2133
         (447 letters)



>FitnessBrowser__Burk376:H281DRAFT_03306
          Length = 434

 Score =  376 bits (965), Expect = e-109
 Identities = 185/414 (44%), Positives = 252/414 (60%), Gaps = 18/414 (4%)

Query: 28  VTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAI 87
           VT EPA   +   A      ALV+RGEY+A+ SDC  CH+  G   + GGL + +P G I
Sbjct: 24  VTAEPAGASDPALA------ALVARGEYLAKASDCAGCHTAVGGQAYGGGLGLTSPFGTI 77

Query: 88  HATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFF 147
            ++NITPD+  GIG YS  DF R+VR GV+PG +RLYPAMPY S+ K+SDDD++ALYA+F
Sbjct: 78  MSSNITPDRRYGIGAYSYEDFARSVREGVSPGNKRLYPAMPYASFSKMSDDDMRALYAYF 137

Query: 148 MQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPG 207
           M G+KPA +P  P+ + +P N RW +  W   FAPT  Y  K  +DA WNRGA++VQGPG
Sbjct: 138 MHGVKPAPEPAPPTKLAFPFNQRWVLYFWQLAFAPTEPYRPKAGRDAQWNRGAFLVQGPG 197

Query: 208 HCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLK 267
           HCG+CHTPRG  F E+  DE+   +L G + D W+ P+L  DP +GLGR  E  +  FLK
Sbjct: 198 HCGACHTPRGPGFQERGYDESSPMYLTGGVNDNWFGPNLTGDPGSGLGRIGEKDLAAFLK 257

Query: 268 TGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQYQAVAAVQ- 326
           TG  A  V +GSM E   +STQ++ D+D  A+A Y+KSLP   Q+    ++  A   +  
Sbjct: 258 TGHGAGLVAFGSMVEQVEDSTQYLTDEDALAMAHYVKSLPA--QKPSGSYEPHAQPDLPT 315

Query: 327 ------DAP---GAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNG 377
                 DAP   GA  Y + CA CHG+ G G P   P LAG  S + +++ S I + + G
Sbjct: 316 RNGNRVDAPQSVGARVYISFCARCHGVQGAGMPNVFPRLAGNPSVITEDTTSLIRLMVEG 375

Query: 378 SQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLR 431
                    P    MP F + L++ ++A VLS++R++WGN+   V AN +  LR
Sbjct: 376 GNSPATISGPPRQAMPGFAQTLTNAQMANVLSWIRTSWGNDARPVTANDIQSLR 429


Lambda     K      H
   0.318    0.133    0.423 

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: 666
Number of extensions: 45
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: 447
Length of database: 434
Length adjustment: 32
Effective length of query: 415
Effective length of database: 402
Effective search space:   166830
Effective search space used:   166830
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: 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