Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__HerbieS:HSERO_RS19685 Length = 456 Score = 227 bits (578), Expect = 6e-64 Identities = 149/415 (35%), Positives = 223/415 (53%), Gaps = 20/415 (4%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTH-YAFNAAP 73 PI + D DG +ID G+GV ++G CNP VVEAI+ Q+ L H N++ Sbjct: 48 PIAMDQAFGVTFKDPDGNTFIDLSAGVGVSSVGRCNPRVVEAIRKQSESLMHSMEVNSSK 107 Query: 74 HGPYLALMEQLSQFVP--VSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHG 131 L ++S+ +P + T G++A E A+K A+ TG+ IIAF GG+HG Sbjct: 108 R---TELAAKISEIMPDGLRGDCITFFTQGGSDALEAAVKFAKRVTGRHQIIAFHGGYHG 164 Query: 132 RTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSA-----DTG-VTCEQ-ALKAMDRLFSV 184 A+ L A Y++ G G V H PYP A DT + EQ A + +D L + Sbjct: 165 IWNASNALTTGTA-YRKGFGPFMGGVIHAPYPYAYRFPFDTSHKSAEQIAGEYVDYLLNT 223 Query: 185 EL-AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243 A +DVAA I EPVQGEGG++ P F Q LR+ CD G L+I+DE+Q+G GRTG+ + Sbjct: 224 PYTAADDVAAVIVEPVQGEGGYVPPSPEFLQILRKACDRSGALLIVDEVQAGAGRTGKMW 283 Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 A G++PD+L K I G MP+ +V R +L A +P G T++ N IS A AL ++ Sbjct: 284 AVEHSGVKPDMLTFGKGIGGDMPMAGLVMRSDLAAKIPDGSQPNTFAANSISAAVALTNI 343 Query: 304 AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAP-- 361 + + D L + ++ ER ++ SP++G + G G M GIE + P Sbjct: 344 SILQDPRLDLVNRAHTLGLEAQ-ERIRSFN-SPWVGEVRGRGLMIGIELVENRETREPLS 401 Query: 362 -AQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 +L K+M+ G+L++P G+ +++R++ LTI ++ +GLDI LA L Sbjct: 402 REKLGKLMDYVVGHGVLMIPCGRYTNVMRVMPSLTIPRSLMFKGLDIFGAGLASL 456 Lambda K H 0.320 0.137 0.402 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: 495 Number of extensions: 30 Number of successful extensions: 6 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: 416 Length of database: 456 Length adjustment: 32 Effective length of query: 384 Effective length of database: 424 Effective search space: 162816 Effective search space used: 162816 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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