Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__HerbieS:HSERO_RS19685 Length = 456 Score = 193 bits (491), Expect = 7e-54 Identities = 123/380 (32%), Positives = 188/380 (49%), Gaps = 42/380 (11%) Query: 25 DDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVPLNFATPARERFIEEFSKLL 84 D G +ID + GV +G NP++VEA++KQ E + + + R + S+++ Sbjct: 61 DPDGNTFIDLSAGVGVSSVGRCNPRVVEAIRKQSESLMH-SMEVNSSKRTELAAKISEIM 119 Query: 85 PPKFG---VVFLQNTGTEAVEVAIKIAKKVTRKPTIVAFTNSFHGRTMGSLSITWNEKYK 141 P + F G++A+E A+K AK+VT + I+AF +HG S ++T Y+ Sbjct: 120 PDGLRGDCITFFTQGGSDALEAAVKFAKRVTGRHQIIAFHGGYHGIWNASNALTTGTAYR 179 Query: 142 KAFEPL--------YPHVRFGKFNVPHE---------VDKLIG------EDTCCVVVEPI 178 K F P YP+ F+ H+ VD L+ +D V+VEP+ Sbjct: 180 KGFGPFMGGVIHAPYPYAYRFPFDTSHKSAEQIAGEYVDYLLNTPYTAADDVAAVIVEPV 239 Query: 179 QGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTAGK 238 QGEGG P +PEFL+ LR+ R GALLI DEVQ G GRTG +WA + GV+PD+ T GK Sbjct: 240 QGEGGYVPPSPEFLQILRKACDRSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGK 299 Query: 239 PVAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREE--DVPGRAER 296 + G +P+ V R D G +TFA N++ A A +L++ D+ RA Sbjct: 300 GIGGDMPMAGLVMRSDLAAKIPDGSQPNTFAANSISAAVALTNISILQDPRLDLVNRAHT 359 Query: 297 IGAELAKALGDTGSRLAVRVKGMGLMLGLEL-----------RVKADQFIQPLLERGVMA 345 +G E + + S V+G GLM+G+EL R K + + ++ GV+ Sbjct: 360 LGLEAQERIRSFNSPWVGEVRGRGLMIGIELVENRETREPLSREKLGKLMDYVVGHGVLM 419 Query: 346 LTAG--VNTLRFLPPYMISK 363 + G N +R +P I + Sbjct: 420 IPCGRYTNVMRVMPSLTIPR 439 Lambda K H 0.320 0.138 0.408 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: 418 Number of extensions: 15 Number of successful extensions: 4 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: 383 Length of database: 456 Length adjustment: 32 Effective length of query: 351 Effective length of database: 424 Effective search space: 148824 Effective search space used: 148824 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 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