Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9KWS5 (491 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 313 bits (802), Expect = 9e-90 Identities = 185/487 (37%), Positives = 263/487 (54%), Gaps = 16/487 (3%) Query: 6 NFVDGKWVESSK--TFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGRTTAAQ 63 +F+DG +VE + + P G +A V+ A +VD A+ A HRA + W + + Sbjct: 11 HFIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKA-WAAMSGTE 69 Query: 64 RVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVDS 123 R LRR A+ M R D E DTGKP +D G F + + + Sbjct: 70 RGRILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGS--LTG 127 Query: 124 HRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTPG 183 + L + Y R+PLGV I WN P + WK APALACGNA+V KPSE TP Sbjct: 128 EHIQLGEDWV---YTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPL 184 Query: 184 TATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMRAAA 243 A +AE++ G+P G++N+V G G G + P ++ ++ TG TG + AAA Sbjct: 185 CALKVAEILHEAGLPAGIYNVVQGLG--EVGASLVTDPRVAKVSLTGSVPTGKKVYAAAA 242 Query: 244 EGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDRFC 303 E +K V+ ELGGK+ +IF D D E + G + F +SGQVC RV+V++ I + F Sbjct: 243 EQMKHVTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFL 302 Query: 304 VALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFGDE 363 L ER+ V P + T GP++S K VL Y E EGA +AGG Sbjct: 303 KRLTERLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLN---- 358 Query: 364 RDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIWTT 423 RD G +++PTV A + DD + REEIFGP+ V F++E E I RAN T +GL+A ++T Sbjct: 359 RD-GFYLQPTVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTR 417 Query: 424 NLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNVCVR 483 +LSRAHRV + G ++N++ + PFGG +SG+GRE ++N YSE+ +V VR Sbjct: 418 DLSRAHRVIAQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVR 477 Query: 484 I-DKESP 489 + D E+P Sbjct: 478 MGDVEAP 484 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: 590 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: 485 Length adjustment: 34 Effective length of query: 457 Effective length of database: 451 Effective search space: 206107 Effective search space used: 206107 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