Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_011383521.1 AMB_RS05630 amino acid decarboxylase
Query= BRENDA::A4Q8H0 (720 letters) >NCBI__GCF_000009985.1:WP_011383521.1 Length = 783 Score = 592 bits (1525), Expect = e-173 Identities = 308/706 (43%), Positives = 431/706 (61%), Gaps = 32/706 (4%) Query: 44 AKGMVTHLEEIGLNIPLFVAVCCE--EELDNAVLPALHGVFELCGKNTQFYGKQLEAAAV 101 A ++ + GL +P+ + V E E++ VL + G L + +F K L + Sbjct: 75 ATELINLMRRRGLEMPIVILVRGERFEDIPVDVLDYIDGYVFLAEETPEFIAKNLVSRLK 134 Query: 102 KYEKDLLPPFFNTLTQYVEMGNATFACPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCN 161 ++ + L PFF L Y E GN + CPGH GG F+ + P GR F + GE +FR D+ N Sbjct: 135 QFAETLKTPFFGALVDYAEEGNQLWTCPGHNGGIFYNRSPIGRIFVEHLGEAVFRDDLDN 194 Query: 162 ADVKLGDLLIHEGLPCAAQQHAAKVFNADKTYFVLNGTSASNKVATNALLTRGDLVLFDR 221 + ++LGDLL HEG AQ+ AAK+F A+KTYFVLNGTSASNK+ +AL+ DLVLFDR Sbjct: 195 SVLELGDLLTHEGPALQAQKEAAKIFGAEKTYFVLNGTSASNKIVLSALVAEDDLVLFDR 254 Query: 222 NNHKSNHHGALIQAGATPVYLETARNPFGFIGGIDAHCFDERYLRQQIRE----VAPERA 277 NNHK+ HHGAL+ G P++LET RN G IG I A FDE+ +R +IR+ PE Sbjct: 255 NNHKAAHHGALLLGGGIPIFLETDRNAMGMIGPIYAEAFDEQAIRAKIRDNPLVKDPEAW 314 Query: 278 NEARPFRLAIIQLGTYDGTIYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLL 337 + RPFR+A+I+ TYDGTIY+A ++++IGHLCDYILFD AW G+ +F P+ + C + Sbjct: 315 KKPRPFRVAVIEQCTYDGTIYSAEHILERIGHLCDYILFDEAWAGFLKFHPLFRGCYGMG 374 Query: 338 LE--LNENDPGIIVTQSVHKQQAGFSQTSQIHKKDKHIKGQSRYCNHKRFNNAFMLHAST 395 L+ L+E+ PGII TQS HKQ AGFSQ SQIH +D+HIKGQSR H+RFN F+LHAST Sbjct: 375 LKDRLDEDSPGIISTQSTHKQMAGFSQASQIHVRDRHIKGQSRRIEHRRFNETFLLHAST 434 Query: 396 SPFYPLFAALDVNAKMHEGKSGQRLWKECVRVGIEARKMLLETCQ-------------LI 442 SPFYPLFA+LDV A+M G+SG+ LW + + +GIE RK + + Sbjct: 435 SPFYPLFASLDVGAQMMRGRSGEVLWDDTIDLGIELRKKVRAIKREFVEKEKDSARHWFF 494 Query: 443 KPFVPDQIDGK-------PWQSYDTETMANDLRFFNFVPGEKWHAFEGYAESQY-FVDPC 494 +PFVPD++ W+ TET+A D R++ F PG +WH F+ + S Y DP Sbjct: 495 EPFVPDRVPSPEGGETMVAWEDLPTETIAADPRYWEFTPGARWHGFKHVSRSGYAMTDPN 554 Query: 495 KLLLTTPGIDTASGNYSDFGIPATILANYLRENGIVPEKCDLNSILFLLTPAEDIAKMQH 554 KL L TPG + +G Y+++GIPA ++A YLREN +VPEK DLNS+LFLLTP + +K Sbjct: 555 KLTLITPGFNRDTGAYAEYGIPAPVVAQYLRENRVVPEKNDLNSMLFLLTPGVESSKAGT 614 Query: 555 LVALIARFEKHIEQDSLLSEVLPAVYKSNEQRYKNYTLRQLCQEMHDLYVSYDVKELQKE 614 L++ + F++ + ++LL + +P + QRY+ ++ LC EMH + +V LQ+ Sbjct: 615 LLSSLVAFKRRHDDNALLDDAIPEFVRRRPQRYRGLRIQDLCAEMHAFFRDRNVSTLQRA 674 Query: 615 MFRKNYFPRIAMNPQDANTEFVRGNIELVSLAKAEGRIAAEGALPYPPGVLCVVPGEIWG 674 F + P + M P DA R ++ + + + +GRIA + YPPG+ ++PGE Sbjct: 675 QFSPEHRPHMVMRPNDAVRMLTRNQVDYLPIDQIDGRIATTLWVVYPPGIATIIPGERLC 734 Query: 675 GAAQ---RYFLALEEGINLLPGFAPELQGVYIQQDEDGWNRAYGYV 717 A+ Y E NL PGF E+QG+Y + + DG R Y YV Sbjct: 735 ERARPMLDYLKMFERSANLFPGFEAEIQGLYREIEPDGSIRFYTYV 780 Lambda K H 0.321 0.138 0.420 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: 1422 Number of extensions: 49 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: 720 Length of database: 783 Length adjustment: 40 Effective length of query: 680 Effective length of database: 743 Effective search space: 505240 Effective search space used: 505240 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 (21.9 bits) S2: 55 (25.8 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