Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate Ac3H11_1486 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1486 Length = 485 Score = 397 bits (1019), Expect = e-115 Identities = 211/486 (43%), Positives = 297/486 (61%), Gaps = 21/486 (4%) Query: 8 LMLENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQ 67 + +++ I GK + Y ++ +P+T EV V + G E+ AAV AA++AFP+W+ Sbjct: 1 MRIQHLIGGKPVESREYFETVNPATQEVLAEVASGGAAEVHAAVAAAKDAFPAWAGLPAP 60 Query: 68 ERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSE 127 ER++++ ++ DL+ + A E+KD G+ + IPR+ NF +FA Sbjct: 61 ERAKLVRKLGDLIAAEVPTLALTETKDTGQVIGQTGKALIPRAADNFYYFAEM------- 113 Query: 128 CTQMD--------HLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKP 179 CT++D HL +YT+ PVGV LISPWN+P TWK+APA+A GNT + K Sbjct: 114 CTRVDGHTYPTPTHL---NYTLFHPVGVCALISPWNVPFMTSTWKVAPALAFGNTAVLKM 170 Query: 180 SELTSVTAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERI 239 SEL+ +TA L +L +AG+P GV+N+V G G GE L +HP+V ISFTGS T RI Sbjct: 171 SELSPLTAARLGELALEAGIPAGVLNVVHGYGKDAGEPLCTHPDVRAISFTGSTATGNRI 230 Query: 240 TQLSAPHCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSI 299 Q A KK S+ELGGK+P ++F DA+LD + A + F+N GE C SRI VQKSI Sbjct: 231 VQ--AAGLKKFSMELGGKSPFVVFADADLDRALDAALFMIFSNNGERCTAGSRILVQKSI 288 Query: 300 YSEFLKRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVD 359 Y++F ++F R+ VG P D +G +IS+AHL KVRSY++ EGA + CG G+ Sbjct: 289 YADFAEKFAARARRIVVGDPLDEKTIVGPMISQAHLAKVRSYIELGPKEGATLLCG-GLG 347 Query: 360 KLSLPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGL 419 LPA Q G F+LPTV D+ + EEIFGPV C++PF+ E E I AN+++YGL Sbjct: 348 TPDLPAHLQKGNFVLPTVFADVDNRMKIAQEEIFGPVACLIPFEDEAEAIRLANDIQYGL 407 Query: 420 AATVWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTE 479 ++ VW+ N+GR HRVA +++G+ + N +R+L PFGG K SG GREG SY+ F E Sbjct: 408 SSYVWTENIGRAHRVAAGIEAGMCFVNSQNVRDLRQPFGGTKGSGTGREGGTWSYEVFLE 467 Query: 480 IKTITV 485 K I V Sbjct: 468 PKNIAV 473 Lambda K H 0.319 0.133 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: 624 Number of extensions: 25 Number of successful extensions: 4 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: 487 Length of database: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 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