Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate Pf6N2E2_3403 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3403 Length = 475 Score = 234 bits (597), Expect = 5e-66 Identities = 162/451 (35%), Positives = 220/451 (48%), Gaps = 20/451 (4%) Query: 4 AHLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLD 63 A S+ + L LT+ +L+ + R +LNAY RA AA A D Sbjct: 8 ASQSIGQLRQALESGTLTSESLVGAQLERIERFNGQLNAYVEAYPQRALGAAIAADRQRA 67 Query: 64 QGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTH 123 G LGPL G+P+++KDL+ + G + GS P + V RL+R I++GKTH Sbjct: 68 AGVHLGPLHGIPIAIKDLFEIDGKAITGGSLAQTPRISRLTATAVQRLERAGAIIMGKTH 127 Query: 124 TVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRV 183 TVEFAFGG G NA GTP NPW HR PGGSS+G+ V++ G A ALGTDT GSVR+ Sbjct: 128 TVEFAFGGWGTNAVMGTPWNPWDHEVHRAPGGSSSGSAVAVAGGLASAALGTDTGGSVRI 187 Query: 184 PASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAA------LDTESQ 237 PA M G VGLKTT G G++ L SLD+ G +T TVED A+ A LD S Sbjct: 188 PAGMCGLVGLKTTRGLVSRHGLIELCPSLDSVGPITHTVEDAAWMLDALLGPDPLDPVSA 247 Query: 238 GLP-----APAPVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLP- 291 P A + V GLR+ V + I P + AA + +++LA G +V PLP Sbjct: 248 KSPVFSAAAGLNLPVAGLRIWVLPQTEREHIAPGVLAAYDQGLEQLAALGMHLVEQPLPT 307 Query: 292 HCEEAFDIFRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVL 351 E+ + GGL ++E A L F R DP V+ RV + + Y+ Sbjct: 308 SLEQCMRV--AGGLMSAEGYASLGSLFERDDLRFDPHVQRRVLSGRAIDAAAYIHLHNQR 365 Query: 352 QRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCAL 411 + VD PT L+ + T P + +NL C++ Sbjct: 366 RAARQAMDEAMSQVDACAFPTNAIGSVPLSQVDEYGT--PLALLG----RFANLLNLCSV 419 Query: 412 TMPVGLDANRMPVGLQLMGPPRAEARLIGIA 442 +PVG D RMPV +Q++G AE ++ IA Sbjct: 420 ALPVGFDEQRMPVSMQIVGRAFAEPLVLRIA 450 Lambda K H 0.320 0.135 0.411 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: 541 Number of extensions: 23 Number of successful extensions: 3 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: 462 Length of database: 475 Length adjustment: 33 Effective length of query: 429 Effective length of database: 442 Effective search space: 189618 Effective search space used: 189618 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