Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 215 bits (547), Expect = 2e-60 Identities = 136/388 (35%), Positives = 204/388 (52%), Gaps = 34/388 (8%) Query: 34 SRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHV-SNVFTNEPALRLAHK 92 + +WD G+ +IDFAGGI V +GH HP +V A+ Q +KL H V E ++LA K Sbjct: 32 AELWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYVKLAEK 91 Query: 93 L---VDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFTV 149 L V +V NSGAEA E A K+AR T K ++ +HGRT +T+ Sbjct: 92 LSGVVPVRGHAKVMLANSGAEALENAMKIARAA------TGKTNVICFDGGYHGRTFYTM 145 Query: 150 NVGGQSK-YSDGFGPKITGITHVPY----------NDLAALKAAV-----SDKTCAVVLE 193 + G++ Y FGP + PY L LK A+ + T A+V+E Sbjct: 146 AMNGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDEALRGLKMAMKADSPAHNTAAIVIE 205 Query: 194 PIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTS 253 P+ GEGG A S+L+ R++CD ++ L++ DEVQ+G GR+GK+FA +H GV PD++T Sbjct: 206 PVLGEGGFYAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTM 265 Query: 254 AKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNA 313 AKS+ G PI+A++ T+ + G TY G+P ACA A AV DV ++L A Sbjct: 266 AKSMADGMPISAIVGTDKYMDASGPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQA 325 Query: 314 KHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGK------AKDIFNAAEREGLM 367 +K K R Q E++ VR LG + L ++ + + A + A+ +GL+ Sbjct: 326 LGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLI 385 Query: 368 ILQAG--PDVIRFAPSLVVEDADIDAGL 393 +L G + +RF + +ED ++ GL Sbjct: 386 LLSCGMYGNTLRFLMPVTIEDEVLEEGL 413 Lambda K H 0.320 0.136 0.400 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: 416 Number of extensions: 23 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: 406 Length of database: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 Effective search space: 147750 Effective search space used: 147750 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 (21.8 bits) S2: 50 (23.9 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