Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >FitnessBrowser__Dyella79:N515DRAFT_3729 Length = 483 Score = 246 bits (628), Expect = 1e-69 Identities = 166/482 (34%), Positives = 251/482 (52%), Gaps = 15/482 (3%) Query: 15 LIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGARM 74 LIDG + W ++ PAT +V A P ++ A+VDAA++AA A W TP R Sbjct: 9 LIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRA 68 Query: 75 RIMLKLQALIREHSKRIAVVLSNEQGKTIADAEG-DIFRGLEVVEH-ACSIGSLQMGEFA 132 R++ +L LI A + S + GK ++ A DI R + + + A +I A Sbjct: 69 RLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSESHA 128 Query: 133 ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTML 192 + G YTLRQP+GV A I+P+N P + W A+A GN V KPSE P + L Sbjct: 129 MEL--GAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAAL 186 Query: 193 LVELAIEAGIPPGVLNVVHG-GKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKR 251 L EL+IEAG PPGVLN+V G G +V AL H+D+KAVSF GST G + A K+ Sbjct: 187 LGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAPRFKK 246 Query: 252 VQSMMGAKNHAVVLPDANREQA-LNALVGAGFGAAGQRCMATS-VVVLVGAAKQWLPDLK 309 + +G KN A+V DA+ A L+ +V +GF G+ C+ S ++V + Sbjct: 247 LSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYL 306 Query: 310 ALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGN 369 A + L+V E TD+G ++S+ ++ I EG ++ G +++PG G Sbjct: 307 AKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALPGPLAGG 366 Query: 370 -FVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAA 428 +V PT+ G+ PE QEIFGPV+ ++ D QA+A+ N +G L+T + Sbjct: 367 WYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSR 426 Query: 429 ARKFQTEIDVGQVGINIPI--PVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTA 486 A +F ++D G V IN + + P F G++ S +G G G + ++F+T+ K + Sbjct: 427 AHRFGAQLDFGIVWINCWLLRDLRTP---FGGAKQSGVGREG--GVEALRFFTEPKNICI 481 Query: 487 RW 488 R+ Sbjct: 482 RY 483 Lambda K H 0.319 0.135 0.397 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: 566 Number of extensions: 30 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: 505 Length of database: 483 Length adjustment: 34 Effective length of query: 471 Effective length of database: 449 Effective search space: 211479 Effective search space used: 211479 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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