Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 347 bits (891), Expect = e-100 Identities = 193/481 (40%), Positives = 287/481 (59%), Gaps = 19/481 (3%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +++G + + GKTF NPAT E+L VA+ GA E A+ AA AL W+ TA ER Sbjct: 14 YVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPA-WRAKTAKER 72 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 A+LR+ +LI+ +E+L+VL +L+ GKP + A + + +I E Sbjct: 73 AAILRRWFELIMAAQEDLAVLMTLEQGKP--------LAEARGEVAYGASFIEWFAEEGK 124 Query: 134 QM-DDVALNYA-------IRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAEL 185 ++ DV ++A ++ P+GV+ I PWN P ++T K+ PALAAG T+V+KPAE Sbjct: 125 RVYGDVIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAED 184 Query: 186 TPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA 245 TP++A LAE+ AGVP GV N+V G P + G LT P V +SFTG T GKI+M Sbjct: 185 TPLSALALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGKILMR 244 Query: 246 SAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYE 305 +A T+K++S ELGG P ++F D++LDE ++ + S + N G+ C+C +R+ V+ Y+ Sbjct: 245 QSADTVKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYD 304 Query: 306 AFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEG 365 AF K K++ VG+ +A G +I+ + E+V + A+ +G + GGKR G Sbjct: 305 AFAAKLAEAVKQIRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGKR-HG 363 Query: 366 LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTN 425 L G F EPTI+TG+T + RV +EEIFGPV + F+TE + + NDT +GL+A ++ Sbjct: 364 L-GGTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSR 422 Query: 426 DLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIK 485 D+ R RVA Q+E G+V +N L PFGG+KQSGIGREG + E + E+ +C+ Sbjct: 423 DIGRVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLCVG 482 Query: 486 L 486 L Sbjct: 483 L 483 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: 615 Number of extensions: 28 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: 486 Length of database: 485 Length adjustment: 34 Effective length of query: 452 Effective length of database: 451 Effective search space: 203852 Effective search space used: 203852 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