Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= BRENDA::Q3UEG6 (513 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 178 bits (451), Expect = 4e-49 Identities = 153/476 (32%), Positives = 223/476 (46%), Gaps = 50/476 (10%) Query: 56 KYQSLAYSRVLAIHKQHLSPVDTAYFRK-PLLLHQGHMEWLFDSEGNRYLDFFSGIV-TV 113 K+ AY+ H H A+ K P+++ +G L D G YLD SG V V Sbjct: 6 KHDPAAYAAADLAHVWHHLVQHQAFAGKGPMIVVEGEGLTLRDINGKEYLDATSGGVWCV 65 Query: 114 SVGHCHPKVSAVAKKQIDRLWHTSSVFFHSPMHEYAEKLSALLPEPLKVIFLVNSGSEAN 173 +VG+ +++ +Q+ + + ++ + P E+A+KL A +P L +L NSGSEAN Sbjct: 66 NVGYGRERIARAVYEQMKAMPYYAATAGNIPYIEFAQKLLAHMPG-LTRAYLSNSGSEAN 124 Query: 174 DLAMVMAR--AHSNHTDI---ISFRGA-YHGCSPYTLGLTNVGIYKME----VPGGIGCQ 223 + A M R AH + I FR YHG + L T K VPG + Sbjct: 125 EKAYKMVRSLAHLSGNPAKKKILFRARDYHGTTLGALSSTGQAERKEWFGPLVPGFVEFP 184 Query: 224 STMCPD-VFRGPWGGIHCRDSPVQTVRDCSCAPDCCQAKERYIEQFKDTLNTSVATSIAG 282 C F + G C DC +A ER IEQ ++ G Sbjct: 185 HACCYRCAFNKTYPG---------------CDIDCARAVERIIEQ-------EGPETVGG 222 Query: 283 FFAEPIQGVNGVVQYPKEFLKEAFALVRERGGVCIADEVQTGFGRLGSHFWGFQTHDVLP 342 EPI GV+ E+ + R G + I DEV G GR G+ F G+Q + V P Sbjct: 223 LIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCGMGRTGTMF-GYQHYGVTP 281 Query: 343 DIVTMAKGIGNGF-PMAAVVTTPEIAKSL----AKRLLHF---STFGGNPLACAIGSAVL 394 DIVTMAKG+ + + P++ TT E+ K+ A ++ +F ST+GG C+ + Sbjct: 282 DIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYFRDISTYGGCAAGCSAALENM 341 Query: 395 EVIEEENLQRNSQEVGTYMLLKFAKLRDEFDIVGDVRGKGLMVGIEMVQDKISRQPLPKT 454 +IEEE L N +G Y+L +L D VGDVRGKGL+ GIE+VQDK ++P+ + Sbjct: 342 AIIEEEKLLDNVNAMGDYLLAGLKELGD-LPYVGDVRGKGLLCGIELVQDKAGKKPMAEG 400 Query: 455 EVNQIHEDCKDMGLLVGRGG----NFSQTFRIVPPMCVTKMEVDFAYEVFRAALIQ 506 +V Q+ + +LVGR F+ I P VT+ +D RAAL++ Sbjct: 401 KVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAPAYVVTRDNIDVILRTLRAALVK 456 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: 531 Number of extensions: 24 Number of successful extensions: 9 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: 513 Length of database: 459 Length adjustment: 34 Effective length of query: 479 Effective length of database: 425 Effective search space: 203575 Effective search space used: 203575 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: 52 (24.6 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