Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate CCNA_03245 CCNA_03245 beta alanine-pyruvate transaminase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Caulo:CCNA_03245 Length = 442 Score = 176 bits (446), Expect = 1e-48 Identities = 126/414 (30%), Positives = 196/414 (47%), Gaps = 43/414 (10%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ- 82 + +H ++ G E E +D G N GH P++ EA+++QA + P Sbjct: 25 FKRHPRMLSSASGMWYRTPESREVLDATSGLWCVNAGHDRPKIREAIQKQAAEMDYAPCF 84 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARA-HTGRKK-----FVAA 136 + P+ +F L I P L+R+F NSG+E+ + ALK A A H R K + Sbjct: 85 NMGHPLAFQFASRLAQITPKGLDRIFFTNSGSESVDTALKIALAYHRARGKGTKTRLIGR 144 Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPY---------------------NDV 175 RG+ G G +SV PK R F L+ V+ +P+ +D+ Sbjct: 145 ERGYHGVGFGGISVGGIPKNRMYFGSLLTGVDHLPHTHGLPGNTCAKGQPENGAHLADDL 204 Query: 176 EALKRAVDEET-AAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRT 234 E + D AAVI+EPV G GV +L R I + LLI DE+ TG GR Sbjct: 205 ERIVALHDASNIAAVIVEPVAGSTGVLIPPKGYLERLRAICDKHDILLIFDEVITGFGRV 264 Query: 235 GKRFAFEHFGIVPDILTLAKAL-GGGVPLGVAVMREEVARSMPKGG-------HGTTFGG 286 G FA E FG+ PD++ +AK L VP G ++ +M G HG T+ Sbjct: 265 GAPFAAERFGVTPDLICMAKGLTNAAVPCGAVAASGKIYDAMMDGADAPIELFHGYTYSA 324 Query: 287 NPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPSPK-IREVRGMGLMVGLELKE 345 +PLA AAG+A + L+ RAA L ++ + + ++ + + +VR +GL+ G+EL+ Sbjct: 325 HPLACAAGLATLETYREDDLFARAAGLEGYWQDAMHSLADARHVVDVRNLGLVAGIELEP 384 Query: 346 KAAPYIARLEKEHRV-----LALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394 + AR + L ++ +I PPL++EK+ ++R+VE +R VL Sbjct: 385 RPGAPTARAMEVFETCFDEGLLIRVTGDIIALSPPLILEKDHIDRMVETIRRVL 438 Lambda K H 0.319 0.137 0.403 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: 439 Number of extensions: 28 Number of successful extensions: 7 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: 395 Length of database: 442 Length adjustment: 32 Effective length of query: 363 Effective length of database: 410 Effective search space: 148830 Effective search space used: 148830 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 (21.7 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