Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= SwissProt::Q9KWS5 (491 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 347 bits (890), Expect = e-100 Identities = 199/478 (41%), Positives = 282/478 (58%), Gaps = 10/478 (2%) Query: 7 FVDGKWVESSKTFQD---VTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGE-WGRTTAA 62 F+DG+WV+++ T + P + + +A V EAD VDAAV A RA + W TTA Sbjct: 5 FIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTAR 64 Query: 63 QRVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVD 122 +R + LR IA ++R ++ E DTGK ++ +D+ + FR +A++ A + Sbjct: 65 ERGELLREIARLLQRDKEHLARTESLDTGKTMA-EGRVDVDDVTSVFRYYANL---ADNE 120 Query: 123 SHRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTP 182 + R+ A ++ +P+GV +I+PWN PLL ++WK+APALA GN VV+KPSE TP Sbjct: 121 AGRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTP 180 Query: 183 GTATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMRAA 242 T L ++E G+P GV NLV G G N +S HPD+ ++FTG +TG IM A Sbjct: 181 LTTIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVS-HPDVDLVSFTGGLETGKKIMAMA 239 Query: 243 AEGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDRF 302 AEGVK V+ ELGGKN V+FAD DF+ +D + A F +SGQVC R+ VE I D F Sbjct: 240 AEGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEF 299 Query: 303 CVALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFGD 362 LA R A+++ + T+ GPL S++HRDKV + E A+ EGA + GG P Sbjct: 300 VAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPT-EP 358 Query: 363 ERDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIWT 422 E +G ++ PTV A + R+V++E+FGP+ V FD+E E IR ANDT YGLA +WT Sbjct: 359 ELADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWT 418 Query: 423 TNLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNV 480 ++ SRA RV+ +R G W+N + + +GG G SGIGRE G L Y E ++ Sbjct: 419 SDASRAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHI 476 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: 650 Number of extensions: 31 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: 496 Length adjustment: 34 Effective length of query: 457 Effective length of database: 462 Effective search space: 211134 Effective search space used: 211134 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 24 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