Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= BRENDA::Q3UEG6 (513 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 185 bits (470), Expect = 2e-51 Identities = 128/397 (32%), Positives = 201/397 (50%), Gaps = 29/397 (7%) Query: 95 LFDSEGNRYLDFFSGIVTVSVGHCHPKVSAVAKKQIDRLWHT-SSVFFHSPMHEYAEKLS 153 L+D++G R +DF GI +++GH HPKV K Q+D+L HT +V + + AEKLS Sbjct: 34 LWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYVKLAEKLS 93 Query: 154 ALLP-EPLKVIFLVNSGSEANDLAMVMARAHSNHTDIISFRGAYHGCSPYTLGLTNVGI- 211 ++P + L NSG+EA + AM +ARA + T++I F G YHG + YT+ + Sbjct: 94 GVVPVRGHAKVMLANSGAEALENAMKIARAATGKTNVICFDGGYHGRTFYTMAMNGKAAP 153 Query: 212 YKMEVPGGIGCQSTMCPDVFRGPWGGIHCRDSPVQTVRDCSCAPDCCQAKERYIEQFKDT 271 Y+ + M V+R P+ + S + +R A Sbjct: 154 YQTDF-------GPMPGTVYRAPYPVPYHGVSEDEALRGLKMAMKA-------------- 192 Query: 272 LNTSVATSIAGFFAEPIQGVNGVVQYPKEFLKEAFALVRERGGVCIADEVQTGFGRLGSH 331 S A + A EP+ G G P FLKE + E + IADEVQ+GFGR G Sbjct: 193 --DSPAHNTAAIVIEPVLGEGGFYAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKM 250 Query: 332 FWGFQTHDVLPDIVTMAKGIGNGFPMAAVVTTPEIAKSLAKRLLHFSTFGGNPLACAIGS 391 F + V PD++TMAK + +G P++A+V T + + L T+ G+P ACA Sbjct: 251 F-AIEHSGVEPDLMTMAKSMADGMPISAIVGTDKYMDASGPNSLG-GTYTGSPTACAAAL 308 Query: 392 AVLEVIEEENLQRNSQEVGTYMLLKFAKLRDEFDIVGDVRGKGLMVGIEMVQDKISRQPL 451 AV +V +EE++ SQ +G + +F++ +++F V +VR G M E+V+ K SR P Sbjct: 309 AVFDVFKEEDILGKSQALGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVESKESRTPK 368 Query: 452 PKTEVNQIHEDCKDMGLLVGRGGNFSQTFRIVPPMCV 488 P+ + + K+ GL++ G + T R + P+ + Sbjct: 369 PELAA-AVTKKAKEKGLILLSCGMYGNTLRFLMPVTI 404 Lambda K H 0.323 0.137 0.424 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: 479 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 513 Length of database: 425 Length adjustment: 33 Effective length of query: 480 Effective length of database: 392 Effective search space: 188160 Effective search space used: 188160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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