Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate PfGW456L13_1397 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-15108 (486 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1397 Aldehyde dehydrogenase (EC 1.2.1.3) Length = 496 Score = 366 bits (940), Expect = e-106 Identities = 199/475 (41%), Positives = 290/475 (61%), Gaps = 4/475 (0%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANER 73 IDG+ P+ G+TF INPAT + L VA G +++ AV A++ G W + ER Sbjct: 22 IDGQRRPAQSGQTFAAINPATSQCLANVAACGEEDVNAAVHNARQVFEAGTWAARSPTER 81 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 VL ++ DLILE +EEL++L+SL+ GKP + +ID+P AA F ++++ + + ++ Sbjct: 82 KQVLLRLADLILENREELALLDSLNMGKPVADAYNIDVPGAAGVFRWYAESLDKLYDQVA 141 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 L R +GV+ + PWN PL + WKLAPALAAGN+V++KPAE +P +A L Sbjct: 142 PSAQNVLATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSVILKPAEQSPFSALRL 201 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA-SAAKTLK 252 AE+ +AGVP GV+N++ G G G AL HPDV+ + FTG T GK M SA LK Sbjct: 202 AELALEAGVPAGVLNVLPGLG-EQTGKALGLHPDVDCLVFTGSTEVGKYFMQYSAQSNLK 260 Query: 253 RLSYELGGKNPNVIFAD-SNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 ++ E GGK+ N++FAD +LD E F NQGEVC SR+ V+R ++ F+E+ Sbjct: 261 QVWLECGGKSANLVFADCQDLDLAAEKAAFGIFFNQGEVCSANSRLLVQRSIHDEFVERL 320 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYF 371 A+ + + GDP D + GA++ R+ +I+ A ++G T + GG++ F Sbjct: 321 KAQAERWLPGDPLDPSSAAGAIVDSRQTARIMKFIQQAEQQGATRICGGRQSIINGSDNF 380 Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431 ++PTI TG+T D + ++E+FGPV+ V FD E L+ ND+ YGL+AS+WT+DL RAH Sbjct: 381 IQPTIFTGVTPDMPLFRDEVFGPVLAVTAFDDEAHALQLANDSVYGLAASLWTDDLNRAH 440 Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 RVA Q+ AG V VN+ D+ PFGG KQSG GR+ LHSF+ Y++L +L Sbjct: 441 RVARQLRAGTVSVNSVDALDVTVPFGGGKQSGFGRDLSLHSFDKYTQLKTTWFQL 495 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: 565 Number of extensions: 21 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: 486 Length of database: 496 Length adjustment: 34 Effective length of query: 452 Effective length of database: 462 Effective search space: 208824 Effective search space used: 208824 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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