Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate BPHYT_RS24640 BPHYT_RS24640 alcohol dehydrogenase
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__BFirm:BPHYT_RS24640 Length = 426 Score = 438 bits (1126), Expect = e-127 Identities = 214/408 (52%), Positives = 268/408 (65%), Gaps = 7/408 (1%) Query: 36 FEQEQAGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPD 95 F Q A A + ALV RG Y+A+ DCVACH+ PFAGGL M TP+G I+ TNITPD Sbjct: 19 FAQTPARAA-DQALVQRGAYLAKAGDCVACHTAPKGKPFAGGLPMTTPMGQIYTTNITPD 77 Query: 96 KSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPAN 155 TGIG Y+ DF RA+R GVA G LYPAMPYPSY K++DDD+KALYA+FM G+ P Sbjct: 78 PQTGIGGYTEEDFARAMREGVAKDGHNLYPAMPYPSYAKVNDDDMKALYAYFMSGVAPVQ 137 Query: 156 QPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTP 215 Q N DI WPLNMRWP+ WN VF Y KP +D WNRGAY++QG GHCGSCHTP Sbjct: 138 QANREPDIKWPLNMRWPLKFWNMVFLDKGVYQDKPGKDVAWNRGAYLIQGLGHCGSCHTP 197 Query: 216 RGLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAV 275 RG+AF EKALDE+G+ FL G LLDGW+A +L + N GLGRW++ + FLKTG N HA Sbjct: 198 RGIAFQEKALDESGSAFLTGGLLDGWFAANLTGEHNVGLGRWNDQDLQAFLKTGANRHAS 257 Query: 276 VYGSMTEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQY--QAVAAVQDAP---- 329 +GSMT NNSTQ + D D+AA++ YLKSLP P++Y QA + P Sbjct: 258 AFGSMTSVINNSTQGLNDTDIAAMSTYLKSLPPAGGSGAPPYKYDPQATKVSLNRPANDA 317 Query: 330 GAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDA 389 GA Y C CHG+DG+G + PL+G + L K+ +S IN+TLNG++ +V G+P Sbjct: 318 GARVYTAYCMHCHGVDGRGFAPMLAPLSGNPNVLEKDPSSLINVTLNGTEDLVIGGIPAP 377 Query: 390 YRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLRGHTDPA 437 Y MP + L+D +IA+VL++VR+ W N AV A+ V KLR T A Sbjct: 378 YPMPKYAPVLNDQQIADVLTFVRAGWNNGAPAVTADDVAKLRKSTHAA 425 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: 679 Number of extensions: 32 Number of successful extensions: 3 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: 426 Length adjustment: 32 Effective length of query: 415 Effective length of database: 394 Effective search space: 163510 Effective search space used: 163510 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