Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate BPHYT_RS25160 BPHYT_RS25160 NAD/NADP-dependent betaine aldehyde dehydrogenase
Query= SwissProt::Q9KWS5 (491 letters) >FitnessBrowser__BFirm:BPHYT_RS25160 Length = 489 Score = 348 bits (892), Expect = e-100 Identities = 201/488 (41%), Positives = 275/488 (56%), Gaps = 11/488 (2%) Query: 5 RNFVDGKWVE--SSKTFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGRTTAA 62 R ++ G +V+ S +TF + P G +A V +A VD AV++ + + EW TA Sbjct: 8 RLYIGGGYVDATSGETFDTLDPATGETLASVQQASAADVDRAVRSAKQG-QREWAALTAM 66 Query: 63 QRVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVD 122 QR LRR + + R + E DTGKP++ +DI G +A LATA ++ Sbjct: 67 QRSRILRRAVDLLRERNDELAALETRDTGKPIAETLAVDIVTGADVIEYYAG-LATA-IE 124 Query: 123 SHRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTP 182 ++ L ++ Y R+PLGV I WN P+ + WK APALA GNA++ KPSE TP Sbjct: 125 GQQIPLRPTSFV--YTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEITP 182 Query: 183 GTATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMR-A 241 +A LAE+ G+P GVFN+V G G G ++ HPDI I+FTG +TG +M A Sbjct: 183 LSALKLAEIFTEAGVPAGVFNVVQGDG--RVGAMLAAHPDIEKISFTGGVETGKKVMSMA 240 Query: 242 AAEGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDR 301 A +K V+ ELGGK+ ++F D + E+ D A F +SGQVC RV+V+R + DR Sbjct: 241 GASSLKEVTMELGGKSPLLVFDDANLERAADIATSANFFSSGQVCTNGTRVFVQRGVLDR 300 Query: 302 FCVALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFG 361 F + ER+K ++V P + T GPL+S+ KVL Y E +QEGA +AGG G Sbjct: 301 FEALVLERVKRIRVGKPTDAATNFGPLVSAAQLHKVLGYIESGKQEGARLVAGGKRLTEG 360 Query: 362 DERDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIW 421 G +VEPTV A DD R+VREEIFGP+ + FD E E I RAN T YGLAA + Sbjct: 361 HFA-GGQYVEPTVFADCRDDMRIVREEIFGPVMSILVFDDEDEAIARANHTAYGLAAGVV 419 Query: 422 TTNLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNVC 481 T NL+RAHRV + GI W+NTW P GG SG+GRE G+ +L Y+ + +V Sbjct: 420 TENLARAHRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQ 479 Query: 482 VRIDKESP 489 V + P Sbjct: 480 VELGPYQP 487 Lambda K H 0.320 0.136 0.417 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: 605 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: 491 Length of database: 489 Length adjustment: 34 Effective length of query: 457 Effective length of database: 455 Effective search space: 207935 Effective search space used: 207935 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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