Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate GFF1133 HP15_1111 betaine aldehyde dehydrogenase
Query= reanno::MR1:199807 (487 letters) >FitnessBrowser__Marino:GFF1133 Length = 493 Score = 182 bits (463), Expect = 2e-50 Identities = 152/487 (31%), Positives = 236/487 (48%), Gaps = 45/487 (9%) Query: 3 HFIKGQWHTGKGHDVASS-NPANGEIIWRGQTATAEQVNAAVDAAREA-QFDWFILGFDA 60 H I GQ+ + + + NPANG+II + A E+V+AAV AAR A + W + D Sbjct: 13 HHINGQYVSSCSSRLFDNVNPANGKIISKVHEAGREEVDAAVKAARAALRGPWGKMTLDE 72 Query: 61 RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYN------- 113 R I+ + A E E +TGKP+ +M I + A N Sbjct: 73 RTSILHKVADGINARFDEFLEGECLDTGKPK--------SMASHIDIPRGAANFKVFADM 124 Query: 114 -KRTGTETND--TPAGRAVLRH---KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVF 167 K TE+ + TP G L + +P GV+ V P+N P L + PAL GN+VV Sbjct: 125 IKNVPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVV 184 Query: 168 KPSELTPKVAELMVTLWEKSGLPAGVLNLVQ--GEVDTGKALASHPQLDGLFFTGSSRTG 225 KPSE TP L+ + +++G+P GV N+V G G L HPQ+DG+ FTG TG Sbjct: 185 KPSEETPTTTTLLGEVMKEAGVPDGVFNVVHGFGGDSAGAFLTEHPQVDGITFTGEIGTG 244 Query: 226 HLLHQQYAGHPGKILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYV 285 ++ + A + ++LE+GG N ++ DI A+ ++SA+ + GQ C R+YV Sbjct: 245 EVI-MKAAAKGIRDISLELGGKNAGVVFADCDIDKAIEGTMRSAFANCGQVCLGTERVYV 303 Query: 286 EQGEQGDALVAKLVEAVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQ-------ANLL 338 E+ D V +L EA + +K+GP + + MG ++S + +++ A ++ Sbjct: 304 ER-SIFDEFVGRLKEAAEGMKIGPPD-DAEADMGPLVSLNHREKVLSYYQKAVDDGATVV 361 Query: 339 SLGGVPLVELMHLQAGTGLVSP----GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIK 394 + GGVP E+ AG V P GL + +AV +E FGP + + ++AI+ Sbjct: 362 TGGGVP--EMPEALAGGAWVQPTIWTGLPEDSAVI---TDEIFGPCCHIRPFDTEEEAIE 416 Query: 395 LANQTRYGLSAGILADSREDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRAS 454 LAN YGL++ I +++ +I AGI+ W PFGG SG R Sbjct: 417 LANSLPYGLASAIWSENITRAHRVAGQIEAGII-WVNSWFLRDLRTPFGGSKQSGIGREG 475 Query: 455 AFYAADY 461 ++ ++ Sbjct: 476 GVHSLEF 482 Lambda K H 0.316 0.133 0.391 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: 603 Number of extensions: 41 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: 487 Length of database: 493 Length adjustment: 34 Effective length of query: 453 Effective length of database: 459 Effective search space: 207927 Effective search space used: 207927 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 (21.6 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