Align Alanine--glyoxylate aminotransferase; AGT; Serine--pyruvate aminotransferase, mitochondrial; SPT; EC 2.6.1.44; EC 2.6.1.51 (characterized)
to candidate 6939183 Sama_3277 Serine--pyruvate transaminase (RefSeq)
Query= SwissProt::P09139 (414 letters) >FitnessBrowser__SB2B:6939183 Length = 376 Score = 275 bits (704), Expect = 1e-78 Identities = 161/371 (43%), Positives = 214/371 (57%), Gaps = 5/371 (1%) Query: 39 PLSIPKRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMFQIMDEIKQGIQYVFQTRNPLTL 98 P P+R+L+GPGPS++ P VL A S +GH+ +MDE+K +QY FQT+N +TL Sbjct: 9 PFMPPRRILMGPGPSDVYPEVLLAQSRPTVGHLDPLFVAMMDELKALLQYAFQTQNEVTL 68 Query: 99 VVSGSGHCAMETALFNLLEPGDSFLVGTNGIWGIRAAEIAERIGARVHQMIKKP-GEHYT 157 VS G MET NL+EPG+ +V NG++G R + ER G V ++ P G Sbjct: 69 AVSAPGSAGMETCFVNLVEPGEKVVVCRNGVFGERMRQNVERCGG-VAVVVDFPWGAPVD 127 Query: 158 LQEVEEGLAQHKPV-LLFLTHGESSTGVLQPLDGFGELCHRYQCLLLVDSVASLGGVPIY 216 Q VE L QH L H E+STG L L + CL +VD+V SLGGV + Sbjct: 128 PQVVEGVLKQHPDASYLAFVHAETSTGALSDAKTLCALAREHNCLSIVDAVTSLGGVELR 187 Query: 217 MDQQGIDILYSGSQKVLNAPPGISLISFNDKAKSKVYSRKTKPVSFYTDITYLSKLWGCE 276 +D+ GID +YSGSQK L+ PG+S +SF+ +A K+ SRKT S++ D T + WG Sbjct: 188 VDEWGIDAIYSGSQKCLSCVPGLSPVSFSPRAVEKLKSRKTPVQSWFLDQTLVMGYWGGS 247 Query: 277 GKTRVIHHTLPVISLYCLRESLALISEQGLENSWRRHREATAHLHKCLRELGLKFFVKDP 336 GK R HHT PV +LY L ESL L++E+GLEN+W RH+ L L +LGL F V D Sbjct: 248 GK-RAYHHTAPVNALYALHESLRLLAEEGLENAWARHQHMHQLLKAGLEKLGLGFVV-DE 305 Query: 337 EIRLPTITTVTVPAGYNWRDIVSYVLDHFNIEISGGLGPSEDKVLRIGLLGYNATTENAD 396 RLP + V +P G + + S +L +N+EI GLG K RIGL+GY A EN Sbjct: 306 AYRLPQLNAVYIPEGVDDAAVRSQLLKGYNLEIGAGLGDLAGKAWRIGLMGYGARAENVA 365 Query: 397 RVAEALREALQ 407 +AL E LQ Sbjct: 366 ICLKALEEVLQ 376 Lambda K H 0.320 0.137 0.412 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: 401 Number of extensions: 17 Number of successful extensions: 4 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: 414 Length of database: 376 Length adjustment: 31 Effective length of query: 383 Effective length of database: 345 Effective search space: 132135 Effective search space used: 132135 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 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