Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate AZOBR_RS03635 AZOBR_RS03635 aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__azobra:AZOBR_RS03635 Length = 471 Score = 384 bits (986), Expect = e-111 Identities = 209/443 (47%), Positives = 284/443 (64%), Gaps = 11/443 (2%) Query: 15 ALSRD--HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGRE 72 A SRD + L P+T+ +G II + EGV ++D G + ++ +A LWCV++G+G E Sbjct: 23 AASRDKAYFLHPYTNLHAHETQGPLIIERGEGVRVFDDSGKEYIEGLASLWCVSLGWGEE 82 Query: 73 ELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLR 132 LV+AATRQMR+LP Y++F +H P ++LA+ + +AP M+ VFF SGSEANDT ++ Sbjct: 83 RLVEAATRQMRKLPTYHVFGHKSHEPGIDLAERLIKLAPVPMSKVFFANSGSEANDTAVK 142 Query: 133 MVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP--Y 190 +V +Y G+P+KK ++ R YHG TVA SL G+ H D PI I H P Y Sbjct: 143 LVWYYNNALGRPEKKKILSRVKAYHGVTVATASLTGLVNNHRDFDLPIARIQHTDCPHHY 202 Query: 191 WYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIRE 250 + E G+ S ++F AE LE IL G E +AA AEP+ GAGGVIVPP TY+ KI+ Sbjct: 203 RFAEPGE-SEEDFATRLAESLEALILAEGPETIAAMFAEPVMGAGGVIVPPATYFAKIQP 261 Query: 251 ILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEI- 309 IL KYDIL +ADEVICGFGRTG ++GSQ G PD++ AK L+SGY+P+ V+V D + Sbjct: 262 ILKKYDILLVADEVICGFGRTGNFWGSQTMGMQPDILTCAKQLSSGYLPISAVMVSDAVY 321 Query: 310 ---VEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQEL 366 VE + G F HG+TYS HPVAAAVA+E ++I E ++ V+A AP Q+R + L Sbjct: 322 RACVEESKKIGTFGHGYTYSAHPVAAAVAIETLKIYEERDLVGHVRA-VAPLFQRRLKAL 380 Query: 367 ADHPLVGEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDTMII 425 ADHPLVGEARGVG++ ALELV +K+T+ F G G + NGLI+RA+GD++ + Sbjct: 381 ADHPLVGEARGVGLIGALELVADKETKTPFDPVGRAGAVVNGLSQENGLIIRAMGDSVAV 440 Query: 426 SPPLVIDPSQIDELITLARKCLD 448 PPLVI I+ + LD Sbjct: 441 CPPLVIGEEDINRMFDRLTTALD 463 Lambda K H 0.320 0.138 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: 588 Number of extensions: 27 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: 456 Length of database: 471 Length adjustment: 33 Effective length of query: 423 Effective length of database: 438 Effective search space: 185274 Effective search space used: 185274 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: 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