Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= reanno::psRCH2:GFF2388 (503 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 225 bits (574), Expect = 2e-63 Identities = 155/475 (32%), Positives = 239/475 (50%), Gaps = 16/475 (3%) Query: 10 VKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRKTPIG 69 V+L++DG+ + + V++PAT A P A+ ++D AVA+ ++AF W TPI Sbjct: 4 VRLIVDGKPLAMA--ETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIE 61 Query: 70 ARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLGEL 129 RA L I ELA +L+AEQGK + +A G++ L AG+ + L Sbjct: 62 DRAAAILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGL-RPAVDVL 120 Query: 130 ANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTM 189 ++ + V+ + +PLGV A I+P+NFP MI +W + GNT V+KPS P+ + Sbjct: 121 KDDDSVRVEVHR--KPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAAL 178 Query: 190 RLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQAGKR 249 R+ E+A A +PPGVLN V G ++ AI HP I + F GST G + + KR Sbjct: 179 RMVEIA-NAHLPPGVLNSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKR 237 Query: 250 VQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALS-VVVLVGEAQAWIPDLVA 308 + +G + AIVLPDA ++ + AFG +GQ C A+ V V A L Sbjct: 238 LTLELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAE 297 Query: 309 KAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYENGNF 368 A+T V G +A + GP+ + D V L + G + G GY F Sbjct: 298 MARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGY----F 353 Query: 369 VGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGAAAR 428 ++ VT M + EE FGP+L V+ + ++A+ NAN NG G ++++ AAA Sbjct: 354 FPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAAL 413 Query: 429 HFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLG-DLGPYGKQVVQFYTQTKTI 482 F + ++ G V +N + P F G++ S +G + G YG ++ Y Q +T+ Sbjct: 414 AFAQRLEAGTVWVNDHASIS-PDVPFGGAKQSGVGTEFGLYG---LEEYMQLQTV 464 Lambda K H 0.318 0.134 0.394 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: 523 Number of extensions: 32 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: 503 Length of database: 469 Length adjustment: 34 Effective length of query: 469 Effective length of database: 435 Effective search space: 204015 Effective search space used: 204015 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