Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BPHYT_RS25160 BPHYT_RS25160 NAD/NADP-dependent betaine aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__BFirm:BPHYT_RS25160 Length = 489 Score = 377 bits (969), Expect = e-109 Identities = 196/476 (41%), Positives = 293/476 (61%), Gaps = 6/476 (1%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +I G +V + G+TFD ++PAT E L +V + AA++D AV++AK+ W +TA +R Sbjct: 10 YIGGGYVDATSGETFDTLDPATGETLASVQQASAADVDRAVRSAKQGQR-EWAALTAMQR 68 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 +LR+ DL+ ER +EL+ LE+ DTGKP + ++DI A +++ I + Sbjct: 69 SRILRRAVDLLRERNDELAALETRDTGKPIAETLAVDIVTGADVIEYYAGLATAIEGQQI 128 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 + + Y R P+GV I WN P+ + WK APALAAGN ++ KP+E+TP++A L Sbjct: 129 PLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEITPLSALKL 188 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASA-AKTLK 252 AEI +AGVP GV N+V G G GA L HPD+ ISFTG TGK +M+ A A +LK Sbjct: 189 AEIFTEAGVPAGVFNVVQGDG--RVGAMLAAHPDIEKISFTGGVETGKKVMSMAGASSLK 246 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 ++ ELGGK+P ++F D+NL+ + ++F + G+VC G+R++V+R + F + Sbjct: 247 EVTMELGGKSPLLVFDDANLERAADIATSANFFSSGQVCTNGTRVFVQRGVLDRFEALVL 306 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR-PEG-LEKGY 370 + K + VG P DA T G L+S +V GYI+ +EG ++ GGKR EG G Sbjct: 307 ERVKRIRVGKPTDAATNFGPLVSAAQLHKVLGYIESGKQEGARLVAGGKRLTEGHFAGGQ 366 Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430 ++EPT+ D R+V+EEIFGPV++++ FD E+E + + N T YGL+A V T +L RA Sbjct: 367 YVEPTVFADCRDDMRIVREEIFGPVMSILVFDDEDEAIARANHTAYGLAAGVVTENLARA 426 Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 HRV ++EAGI W+NTW P GG KQSG+GRE G+ + E Y+ + ++ ++L Sbjct: 427 HRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQVEL 482 Lambda K H 0.318 0.136 0.404 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: 632 Number of extensions: 31 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: 486 Length of database: 489 Length adjustment: 34 Effective length of query: 452 Effective length of database: 455 Effective search space: 205660 Effective search space used: 205660 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: 52 (24.6 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