Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_090438593.1 BLS63_RS01095 aspartate aminotransferase family protein
Query= metacyc::MONOMER-11537 (425 letters) >NCBI__GCF_900100495.1:WP_090438593.1 Length = 416 Score = 343 bits (880), Expect = 6e-99 Identities = 178/421 (42%), Positives = 258/421 (61%), Gaps = 18/421 (4%) Query: 14 AAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNK 73 A++ + +HPI +NA V D G+ +IDF GGI VLN GH HP+I+ AV EQ + Sbjct: 4 ASISNSLAIVHPISLSHGRNAEVWDSTGKRYIDFVGGIGVLNLGHCHPRIVEAVREQAGR 63 Query: 74 LTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVI 133 LTH+ F + +E YV+L E + VP + +L +G+EA ENA+K RAATGR+ VI Sbjct: 64 LTHSAFNAVPHEGYVQLMEALARFVPVSYPLSGMLTNSGAEAAENALKSVRAATGRSAVI 123 Query: 134 AFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFK 193 AF G +HGRT+ TL L GKV PY +G +PG ++ YP+ +GVS + ++A++ER+F Sbjct: 124 AFDGGFHGRTLATLNLNGKVAPYKQKVGTLPGPVYHLPYPSADNGVSREQALAAMERLFS 183 Query: 194 NDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFF 253 + + ++A I+EP+QGEGGF F + LR CD+HGI+LI DEVQ+G GR+G F Sbjct: 184 VEIDQAEVACFIVEPIQGEGGFQALDAAFAQDLRQFCDRHGIVLIIDEVQSGFGRSGQRF 243 Query: 254 AMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVM 313 A ++G+ DL KSIAGG PL V G+ E MDA+ GGLGGTY+G+P+ACAAALA + Sbjct: 244 AFSRLGIEPDLLLLGKSIAGGLPLGAVVGRRELMDALPRGGLGGTYSGNPLACAAALASL 303 Query: 314 EVFEEEHLLDRCKAVGERLVTGLKAIQAKY---------PVIGEVRALGAMIAVELFENG 364 + +L A L G I+A+Y P++G + +GAM +EL Sbjct: 304 TEMSDANL-----ATWGELQAG--TIEARYQRWQGEPWAPLLGRLTGVGAMRGIEL--RS 354 Query: 365 DSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAE 424 P + +A ++ AR++GL+L+ G +++R+L PLT +L++G I+E C A Sbjct: 355 ADGGPGSERLAALLGSAREQGLLLMPSGKARHIIRLLAPLTCERERLEEGFDILERCLAG 414 Query: 425 L 425 L Sbjct: 415 L 415 Lambda K H 0.320 0.137 0.394 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: 510 Number of extensions: 18 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: 416 Length adjustment: 32 Effective length of query: 393 Effective length of database: 384 Effective search space: 150912 Effective search space used: 150912 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: 50 (23.9 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