Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 329 bits (844), Expect = 1e-94 Identities = 184/487 (37%), Positives = 280/487 (57%), Gaps = 11/487 (2%) Query: 17 PSQLLNYIDGNFVTSASS--FANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGK 74 P Q L YI G +V ++S+ F +INP NG++++ V EA A + AV +A+ + W Sbjct: 5 PRQQL-YIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQR-IWAA 62 Query: 75 LSVQDRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKT 134 L+ +RA ++ + D ++ R +E E DTG+P+ + R++DI +A LA Sbjct: 63 LTGIERARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPA 122 Query: 135 SHTDLFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPS 194 + + S + YT R+PLGV+ I WN P+ + WK APALA GN ++ KPS Sbjct: 123 IEGEQIPLRDS----SFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPS 178 Query: 195 EESPSSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTI 254 E + SA LAE+ +AG+P GVFN++ G G G +T+HP I+ ++FTG TG + Sbjct: 179 EVTSLSALKLAEIFSEAGLPDGVFNVLTGSGA-GVGALITEHPRIAKVSFTGGVATGKKV 237 Query: 255 M-KAVADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRS 313 M A + +K+V+ ELGGK+ ++ DADLD A + + ++F +SGQVC RV+V Sbjct: 238 MASAASSSLKDVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAG 297 Query: 314 IFDEFVSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGV 373 + F + L +R+ +G P Q+ N GPL+S H + VL Y GA ++ GG Sbjct: 298 LKAAFEAKLLERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGER 357 Query: 374 PKFNDERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLA 433 E +GA+V PTI++ SD V EEIFGPV + + DEDEVI R ND+ YGLA Sbjct: 358 VT-EGEYAKGAFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLA 416 Query: 434 CAIWTTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDI 493 + T +L+RAHR+ ++ G+ W+NTW + P GG K SG+GRE G S+ Y+ + Sbjct: 417 AGVVTADLARAHRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRV 476 Query: 494 ANICIKI 500 ++ +++ Sbjct: 477 KSVQVEL 483 Lambda K H 0.318 0.135 0.405 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: 579 Number of extensions: 25 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: 500 Length of database: 490 Length adjustment: 34 Effective length of query: 466 Effective length of database: 456 Effective search space: 212496 Effective search space used: 212496 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