Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_076948621.1 C1M55_RS28045 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q88RB9 (425 letters) >NCBI__GCF_002893965.1:WP_076948621.1 Length = 457 Score = 379 bits (973), Expect = e-109 Identities = 197/426 (46%), Positives = 264/426 (61%), Gaps = 7/426 (1%) Query: 5 NESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVV 64 + +L +RR AA+P G+ I+V A V+DV+ IDF GIAV G+ P+VV Sbjct: 32 SRALAKRRSAALPAGLTSGSSIYVAAAGGGVVVDVDDNSFIDFGSGIAVTTVGNSAPRVV 91 Query: 65 AAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIAR 124 QL + +HTCF YE Y+E+CE +N+L PGD +K+T L TGSEA+ENAVK AR Sbjct: 92 ERTTRQLGQFTHTCFLANPYEGYLEVCEALNRLTPGDHEKRTALFNTGSEALENAVKYAR 151 Query: 125 AATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRA------LFPSELHG 178 AATGR V+ F +HGRT+MT+ +T K PY A G ++R +PS Sbjct: 152 AATGRPAVVVFDHAFHGRTLMTMTMTAKNQPYKATFGPFAPEVYRVPMAYPYRWPSGPEN 211 Query: 179 ISVDDAIASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLI 238 + D+A A +AA+++EP+QGEGGF+ +KR+ C + GIL++ Sbjct: 212 -AADEAFAQFRLAIDTQIGAESVAAVVVEPIQGEGGFIVPAPGFLKRISEFCRERGILVV 270 Query: 239 ADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGT 298 ADEVQTG RTG++FA E PD+ T AK +AGG PLA V G+A+ MDA PGG+GGT Sbjct: 271 ADEVQTGIARTGSWFASESEDFVPDIITTAKGLAGGMPLAAVTGRADVMDAAHPGGIGGT 330 Query: 299 YAGSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAV 358 Y+G+P+AC AALAV E E E LLDR+K +G+ LT GL EI IIGD+RG G+MIA+ Sbjct: 331 YSGNPVACEAALAVFETIEMEGLLDRAKDIGDILTTGLSEIASDTDIIGDIRGRGAMIAI 390 Query: 359 EVFEKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIE 418 E+ PN AV Q+V+ A GL+LL+ GTYGNV+R L PL+ D LL +GL I+ Sbjct: 391 ELVHDEDKAPNREAVAQIVSYAHAHGLLLLTAGTYGNVVRFLPPLSISDELLTEGLGILR 450 Query: 419 ECFAEI 424 + A + Sbjct: 451 DAVAAV 456 Lambda K H 0.320 0.138 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: 615 Number of extensions: 28 Number of successful extensions: 2 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: 457 Length adjustment: 32 Effective length of query: 393 Effective length of database: 425 Effective search space: 167025 Effective search space used: 167025 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 24 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