Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)
Query= SwissProt::Q9KWS5 (491 letters) >FitnessBrowser__Keio:14450 Length = 490 Score = 353 bits (907), Expect = e-102 Identities = 202/492 (41%), Positives = 288/492 (58%), Gaps = 16/492 (3%) Query: 1 MKQYRNFVDGKWVE--SSKTFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGR 58 M + + ++ G + S +TF+ + P +G+V+A V A R+ VD AVK+ + + W Sbjct: 4 MAEQQLYIHGGYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQG-QKIWAS 62 Query: 59 TTAAQRVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILAT 118 TA +R LRR + + R + E DTGK S +T+DI G +A ++ Sbjct: 63 MTAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIPA 122 Query: 119 APVDSHRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPS 178 ++ ++ L + ++ Y R+PLGVV I WN P+ + WK APALA GNA++ KPS Sbjct: 123 --LEGSQIPLRETSFV--YTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPS 178 Query: 179 EDTPGTATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTI 238 E TP TA LAE+ G+P GVFN++ G G + G+++++HP I+ ++FTG +G + Sbjct: 179 EVTPLTALKLAEIYSEAGLPDGVFNVLPGVGAET-GQYLTEHPGIAKVSFTGGVASGKKV 237 Query: 239 M-RAAAEGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVE-- 295 M +AA +K V+ ELGGK+ ++F D D + D M A F +SGQVC RV+V Sbjct: 238 MANSAASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAK 297 Query: 296 -RPIFDRFCVALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAG 354 + F++ +A ERI+A V P T GPL+S HRD VL Y ++EGA L G Sbjct: 298 CKAAFEQKILARVERIRAGDVFDPQ---TNFGPLVSFPHRDNVLRYIAKGKEEGARVLCG 354 Query: 355 GGVPRFGDERDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRY 414 G V + GD DNGAWV PTV SDD +VREEIFGP+ + ++SE EVIRRANDT Y Sbjct: 355 GDVLK-GDGFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDY 413 Query: 415 GLAATIWTTNLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFY 474 GLAA I T +L+RAHRV + GI W+NTW P GG SGIGRE G+ +L Y Sbjct: 414 GLAAGIVTADLNRAHRVIHQLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVMTLQSY 473 Query: 475 SELTNVCVRIDK 486 +++ ++ V + K Sbjct: 474 TQVKSIQVEMAK 485 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: 576 Number of extensions: 34 Number of successful extensions: 6 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: 490 Length adjustment: 34 Effective length of query: 457 Effective length of database: 456 Effective search space: 208392 Effective search space used: 208392 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