Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 178 bits (451), Expect = 3e-49 Identities = 128/372 (34%), Positives = 180/372 (48%), Gaps = 9/372 (2%) Query: 18 DVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAI 77 D+ AA + D++ LS G P P PVR AA AALH Y+ G PELR A+ Sbjct: 19 DIHFAAWTAKGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELRAAL 78 Query: 78 AADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGC 137 A D RR G+ VEP+ V++ G+ G A L +AGD V + P Y Y + A G Sbjct: 79 ARDVARRTGLPVEPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGA 138 Query: 138 EVVEI-PCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASD 196 +V + P R P A + A + P R + +A+PANPTG V+ EEL A+A D Sbjct: 139 TLVPVAPDAATLRLDPAA-LAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRHD 197 Query: 197 VRLISDEVYHGLVYQGAPQTSCAW--QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRR 254 + +++DEVY L + P A + V +NS SK +AMTGWR GW++ P L Sbjct: 198 LWVVADEVYASLTFD-RPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVA 256 Query: 255 AVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI-GIDRL 313 + L P Q AA+ A A A Y R + L+ L + G+ L Sbjct: 257 HMGTLALCMLYGLPGFVQQAALVAVEQGDEAVA-AMREGYRRRRDIALEALGSVPGLRCL 315 Query: 314 APTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGD 373 P G F + DV ++ F +L +TGV++ F A G VR+SFA + Sbjct: 316 KPEAGMF-MLVDVRGTGLPTMEFAWRLFRETGVSVLDAGAFGPAAAGC-VRLSFAVSEAE 373 Query: 374 IEEALRRIGSWL 385 + EA RRI +++ Sbjct: 374 LAEACRRIAAFV 385 Lambda K H 0.321 0.136 0.416 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: 447 Number of extensions: 25 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: 388 Length of database: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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