Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__BFirm:BPHYT_RS29875 Length = 483 Score = 380 bits (975), Expect = e-110 Identities = 197/464 (42%), Positives = 282/464 (60%), Gaps = 4/464 (0%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74 IDGK +P G+ +INPATEE + VA+G AA++D AV+AA+ AL W + ER Sbjct: 14 IDGKRLPPGTGEYSVDINPATEEPIALVAQGSAADVDTAVRAARAALK-VWNGIRTAERA 72 Query: 75 AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQ 134 +L ++ L+ EEL+ LESLD GKP DIP A +++ + I + Sbjct: 73 RILMRLAGLMRANLEELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKINGQVVP 132 Query: 135 MDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLA 194 + AL Y +R PVGV+ I PWN PL++ WK+APALA G T+++KPAE+TP+TA + Sbjct: 133 VRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTALRIG 192 Query: 195 EICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRL 254 E+ +AGVP GV+N+V G G G AL HP V+ ++FTG + G+ I+ AA KR+ Sbjct: 193 ELALEAGVPPGVLNIVTGKG-RVVGDALVAHPGVDKVTFTGSPSVGRGILQGAAGNFKRV 251 Query: 255 SYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAK 314 + ELGGK+ N+IF D+NLD + F N G+VC GSRI R Y+ +E+ A+ Sbjct: 252 TLELGGKSANLIFPDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAAR 311 Query: 315 TKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEP 374 K + VGDP +T +G LIS + V GY++ EG +++TGG R E+G+F+EP Sbjct: 312 AKSIKVGDPSSRETSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVG--ERGFFVEP 369 Query: 375 TIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVA 434 T+ + + R+ +EEIFGPV +VI F+ E + + N T Y L+A VW+ D+ R HRVA Sbjct: 370 TVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHRVA 429 Query: 435 GQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 + AG VW+NT+ D+R P+GG SG GRE G + E ++E Sbjct: 430 RDLRAGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENFTE 473 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: 621 Number of extensions: 30 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: 483 Length adjustment: 34 Effective length of query: 452 Effective length of database: 449 Effective search space: 202948 Effective search space used: 202948 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