Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6938540 Sama_2643 putative aminotransferase (RefSeq)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__SB2B:6938540 Length = 460 Score = 169 bits (429), Expect = 1e-46 Identities = 123/411 (29%), Positives = 202/411 (49%), Gaps = 40/411 (9%) Query: 30 RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVF--TNEPAL 87 R EG +WD G +L+D G+ ++G+ ++ A Q Q + +N F T+EPA+ Sbjct: 40 RAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAI 99 Query: 88 RLARKLVDAT--FAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRT 145 RLA K+ RVF SG+EAN+ ++ RRY + P K II+ N++HG T Sbjct: 100 RLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGST 159 Query: 146 LFTVNVGGQPKYSDGFGPKFEGITHV--PY---------------NDLEALKAAI----S 184 + ++GG GI H+ PY +AL+A I Sbjct: 160 VAGASLGGMGFMHQQGDLPIPGIVHIDQPYWFGEGRDMSPEAFGIKTAQALEAKILELGE 219 Query: 185 DKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHY 244 DK A + EP QG GGV+ +Y +++ +++N L + DEV SG GR G FA Sbjct: 220 DKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQTL 279 Query: 245 GVVPDILSSAKSLGGGF-PIGAMLTTGEIAKHL-SVG---THGTTYGGNPLASAVAEAAL 299 G+ PD+++ AK + G+ P+G ++ + +A L S G HG TY G+P+A+AVA + Sbjct: 280 GLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEFAHGFTYSGHPVAAAVALENI 339 Query: 300 DVINTPEVLDGVKAKHERF-KSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKAR--- 355 ++ ++D V+ + + RLQ + + + E+RGMG++ L + R Sbjct: 340 RILEEERLVDKVRTDTGPYLQDRLQTL-SAHPLVGEVRGMGMVGAIELVADKHSMVRFGS 398 Query: 356 -----DVLNAAEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVA 401 + A E+ +V++A D + +P L I EIDE + + +A++ Sbjct: 399 EISAGMLCREACIESGLVMRAVGDTMIISPPLCITRDEIDELIFKASQALS 449 Lambda K H 0.318 0.135 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: 461 Number of extensions: 19 Number of successful extensions: 5 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: 406 Length of database: 460 Length adjustment: 32 Effective length of query: 374 Effective length of database: 428 Effective search space: 160072 Effective search space used: 160072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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