Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 370 bits (950), Expect = e-107 Identities = 197/476 (41%), Positives = 294/476 (61%), Gaps = 5/476 (1%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +I G +V + +TF++INPA E L VAE GAA+++ AV++A++ W +T ER Sbjct: 10 YIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQR-IWAALTGIER 68 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 ++R+ DL+ ER +EL++LE+LDTGKP + S+DI A +++ I E Sbjct: 69 ARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEGEQI 128 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 + D + Y R P+GV+ I WN P+ + WK APALAAGN ++ KP+E+T ++A L Sbjct: 129 PLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSALKL 188 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAA-KTLK 252 AEI +AG+PDGV N++ G G GA +TEHP + +SFTG TGK +MASAA +LK Sbjct: 189 AEIFSEAGLPDGVFNVLTGSGA-GVGALITEHPRIAKVSFTGGVATGKKVMASAASSSLK 247 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 ++ ELGGK+P +I D++LD + + ++F + G+VC G+R++V AF K + Sbjct: 248 DVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEAKLL 307 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR-PEG-LEKGY 370 + + + +GDP +T G L+S H V YI G +L GG+R EG KG Sbjct: 308 ERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEYAKGA 367 Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430 F+ PTI + + D +V EEIFGPV++++ + E+EV+ + NDT YGL+A V T DL RA Sbjct: 368 FVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADLARA 427 Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 HR+ ++EAGI W+NTW + P GG KQSGIGRE G+ S Y+ + ++ ++L Sbjct: 428 HRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVKSVQVEL 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: 592 Number of extensions: 28 Number of successful extensions: 5 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: 490 Length adjustment: 34 Effective length of query: 452 Effective length of database: 456 Effective search space: 206112 Effective search space used: 206112 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