Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_018125377.1 B149_RS0111845 aspartate aminotransferase
Query= BRENDA::D2Z0I0 (402 letters) >NCBI__GCF_000375485.1:WP_018125377.1 Length = 391 Score = 441 bits (1135), Expect = e-128 Identities = 215/391 (54%), Positives = 279/391 (71%), Gaps = 5/391 (1%) Query: 7 FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66 F +V +LP YVFA VNELK ++R +G DI+DLGMGNPD+P +HI+DKL E A RP Sbjct: 4 FARVHRLPPYVFAQVNELKMKMRHQGADIIDLGMGNPDVPTPKHILDKLSEAAYRPGNSR 63 Query: 67 YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126 YSASKGI LRKAI D+YKRRY V LD + +T+GAKEG +HL L ML PGD V+ P+ Sbjct: 64 YSASKGIKGLRKAIADWYKRRYDVYLDKDMETCVTMGAKEGLAHLALVMLTPGDVVLAPD 123 Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186 P YPIH YA II G D VPI + DF E L + S+ +PK ++++FPHNPTT Sbjct: 124 PAYPIHPYASIIAGADVRRVPIGKDRDFFE----DLKVAVTHSWPRPKLLIINFPHNPTT 179 Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246 CVD+ FFQ +V AK+ ++++HD AYAD FDGY PS LQ +GA DV VE +S++K Sbjct: 180 ECVDIAFFQRIVDFAKEHELYVIHDLAYADFTFDGYEAPSFLQADGAKDVGVEFFSLTKS 239 Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306 +SMAG RV F GN+ +++ L +KSYLDYG++TPIQVA+ AL E V + +IY+ Sbjct: 240 YSMAGMRVGFCCGNQDMVQALTRIKSYLDYGIYTPIQVAATHALNGDQECVTEIMDIYKD 299 Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEV-GMNSLDFSLFLLREAKVAVSPGIGFG 365 RRD L EGLNR+GWEV+ PK +MF+WA++PEE M S++FS LL+EA+VAVSPG+GFG Sbjct: 300 RRDALCEGLNRIGWEVEPPKATMFLWAQIPEEFRHMGSVEFSKMLLKEAEVAVSPGLGFG 359 Query: 366 EYGEGYVRFALVENEHRIRQAVRGIKKALDK 396 +YG+ +VRFA VEN HR QA+R ++K K Sbjct: 360 QYGDDHVRFAFVENRHRTNQAIRNLRKFFAK 390 Lambda K H 0.322 0.141 0.425 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: 513 Number of extensions: 22 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: 402 Length of database: 391 Length adjustment: 31 Effective length of query: 371 Effective length of database: 360 Effective search space: 133560 Effective search space used: 133560 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 10 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