Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_007727077.1 C1M55_RS03290 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q88RB9 (425 letters) >NCBI__GCF_002893965.1:WP_007727077.1 Length = 454 Score = 357 bits (915), Expect = e-103 Identities = 181/421 (42%), Positives = 265/421 (62%), Gaps = 10/421 (2%) Query: 7 SLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAA 66 +L +RR V GV P++V A ++DV+G LID GIAV + G +P VV+A Sbjct: 25 ALAERRKKVVGAGVASTLPVYVADADGGVIVDVDGNSLIDLGAGIAVTSVGASNPAVVSA 84 Query: 67 VQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAA 126 VQ+Q+ +HTCF V YE YVE+ E++ +L PGD +K+++L +G+EAVENAVKIAR A Sbjct: 85 VQDQVAHFTHTCFMVAPYEGYVEVAERLAELTPGDHEKRSVLFNSGAEAVENAVKIARHA 144 Query: 127 TGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRA--LFPSELHGISVDDA 184 TGR V+ F YHGRT +T+ LT K +PY +G G ++R +P G++VD + Sbjct: 145 TGRDAVVVFDHAYHGRTNLTMALTSKSMPYKSGFGPFAPEVYRVPMSYPYR-EGLNVDGS 203 Query: 185 IASVER-------IFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILL 237 + E+ + + + AAI++EP+QGEGGF+ + + L A ++G++ Sbjct: 204 KITGEQAAQRAITMIEKQVGAANTAAILIEPIQGEGGFIVPAEGFLPTLVAWAKENGVVF 263 Query: 238 IADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGG 297 IADEVQ G RTG +FA + G+ PDL T AK IAGG PLA V G+AE +DA+ PGGLGG Sbjct: 264 IADEVQAGFARTGAWFASDHEGIVPDLVTLAKGIAGGMPLAAVTGRAELIDAVHPGGLGG 323 Query: 298 TYAGSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIA 357 TY G+P+ACAAALA I+ E L R++ + + + + K+ +IGDVRG G+M+A Sbjct: 324 TYGGNPVACAAALASIDQMRELDLCGRARTIESTVVGRMNALAKELDVIGDVRGRGAMLA 383 Query: 358 VEVFEKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAII 417 +E+ + G P+A ++ A+ G+++L+CGTYGNV+R+L PL + LLD L ++ Sbjct: 384 IELVKPGGQEPDADITKKIAAECLAAGVVILTCGTYGNVIRLLPPLVISEELLDDALTVL 443 Query: 418 E 418 E Sbjct: 444 E 444 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: 588 Number of extensions: 27 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: 454 Length adjustment: 32 Effective length of query: 393 Effective length of database: 422 Effective search space: 165846 Effective search space used: 165846 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