Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BPHYT_RS28885 BPHYT_RS28885 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__BFirm:BPHYT_RS28885 Length = 485 Score = 408 bits (1049), Expect = e-118 Identities = 214/478 (44%), Positives = 301/478 (62%), Gaps = 11/478 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 H I+GK + D F+ +NPAT+E L VA GGA E+D AV+AAK A W A E Sbjct: 5 HLINGKASAAKD--YFETVNPATQEVLAEVARGGAEEVDAAVRAAKDAFPA-WAAKPAAE 61 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R ++RK+G+LI + ++S E+ DTG+ + +PRAA NF +F++ + Sbjct: 62 RAKLVRKLGELIAKNVPDISETETKDTGQTISQTRKQLVPRAADNFSYFAEMCTRVDGH- 120 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 T D LNY + PVGV LI+PWN+P + TWK+AP LA GNT V+K +EL+P+TA++ Sbjct: 121 TYPTDTHLNYTLFHPVGVCALISPWNVPFMTATWKVAPCLAFGNTAVLKMSELSPLTASM 180 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L + +AG+P GV+N+VHGFG ++ G L HPDV+A+SFTG T TG I+ +A LK Sbjct: 181 LGNLALEAGIPAGVLNVVHGFGKDT-GEPLVAHPDVHAVSFTGSTATGNRIVQTAG--LK 237 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 + S ELGGK+P VIF D++ + ++ + F N GE C GSRI V+R Y F E+F+ Sbjct: 238 KFSMELGGKSPFVIFDDADFERALDAAVFMIFSNNGERCTAGSRILVQRSIYARFAERFI 297 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG----KRPEGLEK 368 + K L VGDP T VG +IS H +V YI+L +EG T+ GG + P+ + K Sbjct: 298 ERAKRLTVGDPLADSTIVGPMISQGHLAKVRSYIELGPKEGATLACGGLDMPELPDAMRK 357 Query: 369 GYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLR 428 G F++PT+ + R+ +EEIFGPV +IPFD E + ++ ND YGLS+ +WT + Sbjct: 358 GNFVQPTVFVDVDNRMRIAQEEIFGPVACLIPFDDEADAIKLANDISYGLSSYIWTENTG 417 Query: 429 RAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 RA RVA +EAG+ +VN+ +RDLR PFGG K SG+GREGG S+E + E N+C+ L Sbjct: 418 RALRVAAAVEAGMCFVNSQNVRDLRQPFGGTKASGVGREGGTWSYEVFLEPKNVCVSL 475 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: 642 Number of extensions: 23 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: 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