Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate BPHYT_RS10075 BPHYT_RS10075 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__BFirm:BPHYT_RS10075 Length = 433 Score = 366 bits (940), Expect = e-106 Identities = 189/429 (44%), Positives = 254/429 (59%), Gaps = 23/429 (5%) Query: 22 GLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHSLAGK---------- 71 G LA T A P A + A ++RG Y+A+ +DC CH+ A + Sbjct: 4 GALASSYTAASAAPGSATSA----DTAQIARGAYLAKAADCAGCHTAAPRVVRPGTAPIP 59 Query: 72 -APFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYP 130 APFAGGL MA+P G I+++NITPD GIG YS DF A+R GVA GG+RLYPAMPYP Sbjct: 60 AAPFAGGLGMASPFGTINSSNITPDPQAGIGLYSYDDFAHALRDGVARGGKRLYPAMPYP 119 Query: 131 SYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKP 190 S+ K+ DDD+ ALYA+FM G++P P P+ +P+P N RW + W+ F P + + Sbjct: 120 SFAKIDDDDMHALYAYFMHGVRPVATPAPPTRLPFPFNQRWALMFWDWAFVPGERFKPEA 179 Query: 191 DQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDP 250 +DA WNRGAY+VQ GHCG+CHTPRG A+ E+ EA +L G D W+AP+L D Sbjct: 180 GRDAQWNRGAYLVQSLGHCGACHTPRGPAYEERGYTEASPLYLTGGTNDHWFAPNLTADT 239 Query: 251 NTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDP 310 +GLGR S I FLK G V +GSM + +STQ++ D DLAAIA YLKSLP Sbjct: 240 GSGLGRSSAEDIAAFLKHGHGGGLVTFGSMVQVVEDSTQYLDDADLAAIATYLKSLPPRA 299 Query: 311 Q----RDGAPWQYQAVAAVQ----DAPGAHTYATRCASCHGLDGKGQPEWMPPLAGATSA 362 Q G+ Q+V A++ + PGA YAT CA CH DG G P+ P LAG + Sbjct: 300 QSGHFNAGSRGALQSVEALKTGELERPGAGIYATYCARCHQSDGAGVPQKYPRLAGNPAV 359 Query: 363 LAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAV 422 LA ++ S + + + G G P+ +MPAF ++L+D+E+A VL+++R+TWGN V Sbjct: 360 LAPQTTSLVRLLVEGGGSPNTDGGPEPRKMPAFADKLTDSELAHVLTFIRNTWGNAAEPV 419 Query: 423 DANAVGKLR 431 V +R Sbjct: 420 TTRDVSAVR 428 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: 708 Number of extensions: 30 Number of successful extensions: 5 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: 433 Length adjustment: 32 Effective length of query: 415 Effective length of database: 401 Effective search space: 166415 Effective search space used: 166415 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.
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:
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