Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >FitnessBrowser__Phaeo:GFF919 Length = 450 Score = 169 bits (429), Expect = 1e-46 Identities = 133/407 (32%), Positives = 205/407 (50%), Gaps = 38/407 (9%) Query: 36 VTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKL--THTCFQVLAYEPYVELCEK 93 V D +GR++I+ G+ + G+ + +V+ A+TEQL+KL THT F ++P +L +K Sbjct: 27 VFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFTHT-FGGKTHQPIQDLADK 85 Query: 94 INAKVPGDFAKKTLLVTTGSEAVENSIKIARAATGRAG------VIAFTGAYHGRTMMTL 147 + A VP + A +GS+A + K+ R G +I YHG T+ Sbjct: 86 LAAMVPVEDAY-IFFGNSGSDANDTHYKMLRYYFNAIGKPEKRKIITRERGYHGVTVAAG 144 Query: 148 GLTG---KVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIAS-IERIFKN------DAE 197 LT + + A + + I RA P+ +++ A +ERI +N + Sbjct: 145 SLTSLPANLAHFDAPLEAL--SILRADSPHYYTARQGNETEAQFVERILQNLEDQIISED 202 Query: 198 PRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQ 257 P IAA+I+EP+ G G V P + + L+AL ++GIL+ ADEV G GRTG F Sbjct: 203 PDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICGFGRTGADFGCTT 262 Query: 258 MGVAADLTTFAKSIAGG-FPLAGVC-------GKAEYMDAIAPGGLGGTYAGSPIACAAA 309 MG+ DL TFAK ++ FP++ + + + G G TY+G P ACAAA Sbjct: 263 MGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGYTYSGHPAACAAA 322 Query: 310 LAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFEN----GD 365 L +E++E ++L D VG L T L+ I +P++GEVR G + A+EL N Sbjct: 323 LKTLEIYERDNLFDHAAEVGSYLQTQLREIFTDHPLVGEVRGKGLIAALELVSNKTTGAS 382 Query: 366 SHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLD 412 K A A A+ + +D GLIL + GN + + PL E++D Sbjct: 383 FDKGRAGATAQRL--CQDNGLILRAVA--GNAVALCPPLIITREEVD 425 Lambda K H 0.320 0.137 0.395 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: 442 Number of extensions: 22 Number of successful extensions: 3 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: 425 Length of database: 450 Length adjustment: 32 Effective length of query: 393 Effective length of database: 418 Effective search space: 164274 Effective search space used: 164274 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 Sep 17 2021. 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