Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >FitnessBrowser__Marino:GFF3766 Length = 425 Score = 423 bits (1087), Expect = e-123 Identities = 213/422 (50%), Positives = 278/422 (65%) Query: 4 TNASLMKRREAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLHPKV 63 +N L +E V G + FADHA N+ + D +G+ IDFAGGI VLN GH HPKV Sbjct: 2 SNKELQALKERYVAAGAASPNEQFADHATNAELWDADGKRMIDFAGGIGVLNIGHRHPKV 61 Query: 64 IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENSIKIA 123 + AV QL+KL HTC V+ YE YV+L EK++ VP K +L +G+EA+EN++KIA Sbjct: 62 VEAVKAQLDKLMHTCQTVMPYEGYVKLAEKLSGVVPVRGHAKVMLANSGAEALENAMKIA 121 Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183 RAATG+ VI F G YHGRT T+ + GK PY G MPG ++RA YP HGVS D+ Sbjct: 122 RAATGKTNVICFDGGYHGRTFYTMAMNGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDE 181 Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243 ++ ++ K D+ + AAI+IEPV GEGGFY AP F+K +R +CD++ IL+IADEVQ Sbjct: 182 ALRGLKMAMKADSPAHNTAAIVIEPVLGEGGFYAAPTSFLKEIRKICDENDILMIADEVQ 241 Query: 244 TGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303 +G GRTG FA+E GV DL T AKS+A G P++ + G +YMDA P LGGTY GSP Sbjct: 242 SGFGRTGKMFAIEHSGVEPDLMTMAKSMADGMPISAIVGTDKYMDASGPNSLGGTYTGSP 301 Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFEN 363 ACAAALAV +VF+EE +L + +A+GE+L Q ++ + VR LG M A EL E+ Sbjct: 302 TACAAALAVFDVFKEEDILGKSQALGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVES 361 Query: 364 GDSHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIMEECFS 423 +S P A V KA++KGLILLSCG YGN LR L+P+T DE L++GLAI+EE Sbjct: 362 KESRTPKPELAAAVTKKAKEKGLILLSCGMYGNTLRFLMPVTIEDEVLEEGLAIVEESLK 421 Query: 424 EL 425 E+ Sbjct: 422 EV 423 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: 459 Number of extensions: 13 Number of successful extensions: 1 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: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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