Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__SB2B:6939342 Length = 506 Score = 356 bits (913), Expect = e-102 Identities = 201/481 (41%), Positives = 282/481 (58%), Gaps = 14/481 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI GK+VP + G+ FDN++P + A +I+LA+ AA A + W K + E Sbjct: 21 NFIGGKWVPPVGGEYFDNVSPVDGKVFCQAARSDYRDIELALDAAHAAKDS-WGKTSVTE 79 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L K+ D + + E L+V+E+ + GK + + D+P +F +F+ IR A Sbjct: 80 RSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSA 139 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +D ++Y + P+GV+G I PWN PLL+ WK+APALAAGN VV+KPAE TP + V Sbjct: 140 ADLDANTVSYHLPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPASIMV 199 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L E D +P GV+N+V+GFG AGAAL + ++FTG T G I+ AA+ L Sbjct: 200 LLETIEDL-LPPGVLNVVNGFGA-EAGAALATSKRIAKLAFTGSTEVGNHILKCAAENLI 257 Query: 253 RLSYELGGKNPNVIFA------DSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306 + ELGGK+PN+ FA D+ LD+ IE M +F NQGEVC C SR+ V+ Y+A Sbjct: 258 PSTVELGGKSPNIYFADVMNHEDNYLDKAIE-GMLLAFFNQGEVCTCPSRVLVQESIYDA 316 Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG--KRPE 364 F+EK +A+ K + G P D T+VGA S E Y+++ GY+ + EG +L GG K + Sbjct: 317 FIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKVLMGGEFKLQD 376 Query: 365 GLEK-GYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 G EK GY+++PTI+ G + RV +EEIFGPVV+V F E E L NDT YGL A VW Sbjct: 377 GPEKGGYYIQPTILKGHNK-MRVFQEEIFGPVVSVTTFKDEAEALAIANDTQYGLGAGVW 435 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483 T D+ A R+ I+AG VW+N + FGG K+SGIGRE Y N+ Sbjct: 436 TRDMNLAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQNTKNLL 495 Query: 484 I 484 + Sbjct: 496 V 496 Lambda K H 0.318 0.136 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: 596 Number of extensions: 24 Number of successful extensions: 7 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: 486 Length of database: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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