Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PP_3718 PP_3718 putative aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Putida:PP_3718 Length = 470 Score = 344 bits (882), Expect = 4e-99 Identities = 177/443 (39%), Positives = 271/443 (61%), Gaps = 7/443 (1%) Query: 20 HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAAT 79 H++ + + + E+GA I EG YI D+ GN+ LDA+ G+WC N+G GREE+ A Sbjct: 22 HYMHGYHVFDEHREQGALNIVAGEGAYIRDTHGNRFLDAVGGMWCTNIGLGREEMALAIV 81 Query: 80 RQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWA 139 Q+R+L + N F A+ +EL + +A +AP +NHVF T GS A DT R++++Y Sbjct: 82 DQVRQLAYSNPFSDMANDVAIELCQKLAQLAPGDLNHVFLTTGGSTAVDTAYRLIQYYQN 141 Query: 140 TKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALH-EQGDFPIPGIVHIAQPYWYGEGGDM 198 +G+P KK +I R+N YHGST +S+G A + D+ I H++ P Y DM Sbjct: 142 CRGKPHKKHIIARYNAYHGSTTLTMSIGNKAADRVPEFDYHHDLIHHVSNPNPYRAPDDM 201 Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258 EF + + E KIL +G +NVAAF AEPI G+GGVI+PP+ Y+ ++ ++ YDIL Sbjct: 202 DEAEFLDFLVAEFEDKILSLGADNVAAFFAEPIMGSGGVIIPPEGYFQRMWQLCQTYDIL 261 Query: 259 FIADEVICGFGRTGEWFGS-QYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG 317 F+ADEV+ FGR G +F S + +G PD++ AKGLTS Y+P+G + + I +V+ + G Sbjct: 262 FVADEVVTSFGRLGTFFASEELFGVTPDIITTAKGLTSAYLPLGACIFSERIWQVIAEPG 321 Query: 318 E---FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGE 374 + F HGFTYSGHPV AL+NI I+ E++++ V + YL++R Q L D PLVG+ Sbjct: 322 KGRCFTHGFTYSGHPVCCTAALKNIEIIEREQLLDHVN-DVGSYLEQRLQSLRDLPLVGD 380 Query: 375 ARGVGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDP 433 R + ++A +E V NK ++ F D+ +G GL++R + ++SPPL+I Sbjct: 381 VRCMKLMACVEFVANKASKALFADEVNIGERIHSKAQEKGLLVRPIMHLNVMSPPLIITH 440 Query: 434 SQIDELITLARKCLDQTAAAVLA 456 +Q+DE++ R+C+ +TA + A Sbjct: 441 AQVDEIVETLRQCIIETARELTA 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: 593 Number of extensions: 24 Number of successful extensions: 6 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: 470 Length adjustment: 33 Effective length of query: 423 Effective length of database: 437 Effective search space: 184851 Effective search space used: 184851 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