Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= SwissProt::Q9H2A2 (487 letters) >NCBI__GCF_000009985.1:WP_011384974.1 Length = 479 Score = 271 bits (694), Expect = 3e-77 Identities = 167/483 (34%), Positives = 262/483 (54%), Gaps = 24/483 (4%) Query: 10 LENFIDGKFLPC---SSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSP 66 L+ ++DG ++ S +D +P+T +V RV G D+ A++AA +AFP+W++ Sbjct: 5 LDFYVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPL 64 Query: 67 QERSRVLNQVADLLEQSLEEFAQAESKDQGKTLA-LARTMDIPRSVQNFRFFASSSLHHT 125 ER +L +V E+ L+E A+A S + G L LA+ + +F+ S + + Sbjct: 65 AERLEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYA 124 Query: 126 SECTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSV 185 E Q L V+ PVGV LI+PWN P+ + K+APA+AAG ++ KPSE Sbjct: 125 FERRQGTTL-----VVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEFAPY 179 Query: 186 TAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP 245 +A +L +++ +AGVP GV N+VFG G +G L SHP V ++S TGS + + A Sbjct: 180 SARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMREGAA 239 Query: 246 HCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLK 305 KK+SLELGGK+ II + A+ + I V++ N G+ C SR+FV E Sbjct: 240 TIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDEAEG 299 Query: 306 RFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCG-----EGVDK 360 E + KVG PSDP +G + + +KVR ++ + EGA++ CG EG+DK Sbjct: 300 LAAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPEGLDK 359 Query: 361 LSLPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLA 420 GYF+ PTV + + D M EEIFGPV + + ++ + AN+ YGL+ Sbjct: 360 ---------GYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLS 410 Query: 421 ATVWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEI 480 V++ ++ VA++L++G+V N + PFGG++ SG+GRE + ++ F E Sbjct: 411 GYVYAGDLDEARAVARRLRTGMVHLN-GALSHPGGPFGGIRQSGVGREWGEAGFEEFLES 469 Query: 481 KTI 483 KT+ Sbjct: 470 KTL 472 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: 532 Number of extensions: 27 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: 487 Length of database: 479 Length adjustment: 34 Effective length of query: 453 Effective length of database: 445 Effective search space: 201585 Effective search space used: 201585 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