Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate CCNA_03245 CCNA_03245 beta alanine-pyruvate transaminase
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Caulo:CCNA_03245 Length = 442 Score = 262 bits (669), Expect = 2e-74 Identities = 150/433 (34%), Positives = 232/433 (53%), Gaps = 17/433 (3%) Query: 24 PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83 PFT ++ ++ R+++ A G++ E ++LDA +GLWCVN G+ R ++ +A +Q Sbjct: 18 PFTPNRRF-KRHPRMLSSASGMWYRTPESREVLDATSGLWCVNAGHDRPKIREAIQKQAA 76 Query: 84 ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143 E+ Y F HP + A +A + P+G++ +FFT SGSE+ DT L++ Y +G+ Sbjct: 77 EMD-YAPCFNMGHPLAFQFASRLAQITPKGLDRIFFTNSGSESVDTALKIALAYHRARGK 135 Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM---SP 200 K +IGR GYHG G+S+GG+ + G+ H+ P+ +G G+ Sbjct: 136 GTKTRLIGRERGYHGVGFGGISVGGIPKNRMYFGSLLTGVDHL--PHTHGLPGNTCAKGQ 193 Query: 201 DEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFI 260 E G A+ LE+ + N+AA I EP+ G+ GV++PP Y ++R I K+DIL I Sbjct: 194 PENGAHLADDLERIVALHDASNIAAVIVEPVAGSTGVLIPPKGYLERLRAICDKHDILLI 253 Query: 261 ADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG--- 317 DEVI GFGR G F ++ +G PDL+ +AKGLT+ +P G V +I + + G Sbjct: 254 FDEVITGFGRVGAPFAAERFGVTPDLICMAKGLTNAAVPCGAVAASGKIYDAMMDGADAP 313 Query: 318 -EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEAR 376 E +HG+TYS HP+A A L + RE+ + + A Y Q LAD V + R Sbjct: 314 IELFHGYTYSAHPLACAAGLATLETYREDDLFARA-AGLEGYWQDAMHSLADARHVVDVR 372 Query: 377 GVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQI 436 +G+VA +EL M E CF GL++R GD + +SPPL+++ I Sbjct: 373 NLGLVAGIELEPRPG-----APTARAMEVFETCFDEGLLIRVTGDIIALSPPLILEKDHI 427 Query: 437 DELITLARKCLDQ 449 D ++ R+ L Q Sbjct: 428 DRMVETIRRVLGQ 440 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: 554 Number of extensions: 31 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: 442 Length adjustment: 33 Effective length of query: 423 Effective length of database: 409 Effective search space: 173007 Effective search space used: 173007 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