Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF4212 Psest_4285 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__psRCH2:GFF4212 Length = 452 Score = 161 bits (408), Expect = 3e-44 Identities = 123/414 (29%), Positives = 200/414 (48%), Gaps = 40/414 (9%) Query: 26 VWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY-AFNAAPHGPYLALMEQL 84 +WD++G + +D + G+ +NLG+ +VEA Q L +Y F H P +AL + + Sbjct: 43 LWDSEGHKILDAMAGLWCVNLGYGREELVEAATRQMRELPYYNLFFQTAHPPAVALAKAI 102 Query: 85 SQFVPVSYPLAGM----LTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTL 134 + P AGM T SG+EA + L++ R G K+ +I G+HG T+ Sbjct: 103 ADIAP-----AGMNHVFFTGSGSEANDTVLRMVRHYWAIKGQPAKKVVIGRWNGYHGSTI 157 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHL--PYPSADTGVTC--EQALKAMDRLFS--VELAV 188 A +L G A ++Q G +PG + H+ PY + G E ++ D+L +E+ Sbjct: 158 AGASLGGMKAMHEQSDGPIPG-IEHIDQPYWFGEGGDMSPEEFGVRIADQLEQKILEVGE 216 Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248 + VAAFI EP+QG GG + + ++ IL I DE+ GFGRTG+ F Sbjct: 217 DKVAAFIAEPIQGAGGVIIPPETYWPRIKEILARYDILFIADEVICGFGRTGEWFGSDYY 276 Query: 249 GIEPDLLLLAKSIAGG-MPLGAVVGRKELMAALPKGG---LGGTYSGNPISCAAALASLA 304 G+EPDL+ +AK + G +P+G V+ R E++ L +GG G TYSG+P++ A AL ++ Sbjct: 277 GLEPDLMPIAKGLTSGYIPMGGVIVRDEVVQTLNEGGEFYHGFTYSGHPVAAAVALENIR 336 Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANAD------GS 358 + +E + + + + RW+ P +G GVG + +E Sbjct: 337 ILREEKIVERVKTKTAPYLQ--SRWQELLDHPLVGEARGVGLLGALELVKNKKTRERFAD 394 Query: 359 PAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 P L + E GL++ G + + PL I E ++E + + CL Sbjct: 395 PGVGMLCR--EHCFRNGLVMRAVGDT---MIISPPLVISEEQIDELIGKVRLCL 443 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: 479 Number of extensions: 26 Number of successful extensions: 5 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: 452 Length adjustment: 32 Effective length of query: 384 Effective length of database: 420 Effective search space: 161280 Effective search space used: 161280 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 Apr 09 2024. The underlying query database was built on Sep 17 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