Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate SMa1377 SMa1377 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Smeli:SMa1377 Length = 471 Score = 201 bits (511), Expect = 4e-56 Identities = 153/453 (33%), Positives = 224/453 (49%), Gaps = 31/453 (6%) Query: 5 HLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQ 64 +LS+ + AA +R RE++AV + + L + A AA +DT L+ Sbjct: 6 NLSIRKLAAMVRAREISAVDVTTHFLGRIVAYDDALCGFNVPAPEAALDAAHDLDTYLNA 65 Query: 65 GQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHT 124 G + G L G+P+S+KD V GLP S A +VAR++ GIV+GK + Sbjct: 66 GGEAGALAGIPLSIKDTADVAGLPSAGASASRSGRTATADATVVARMKAAGGIVLGKANC 125 Query: 125 VEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVP 184 E AFGG + + RNPW+ R PGGSS+G+GV++ G L +L TDTAGS+R+P Sbjct: 126 HELAFGGPSFDLPFPPARNPWNLD--RFPGGSSSGSGVTVAAGLCLGSLATDTAGSIRLP 183 Query: 185 ASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPAP 244 A+M G GLK P++GI L++++D G + RT +D F + S G P Sbjct: 184 ATMCGVFGLKPGHDTLPLDGIAVLAATMDHVGPVARTADDTRILFDVMAGRSPGSPFVGS 243 Query: 245 VRVQGLRVGVPTNHFWDD---IDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFR 301 ++ GLR+GVP N WD I P + AA++ A++ GA +V LP E+ F Sbjct: 244 LK--GLRIGVPENE-WDVGRLIHPDVRAAIDGAIEVARSEGADIVPLRLPSLED----FH 296 Query: 302 RGG--LAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYL---RRKAVLQRCGA 356 G L E+AA ++ + R R E ++ ++ R + VL++ Sbjct: 297 APGTVLMMCEVAAEHAASVRAAWDKFGAIFRARALVGEGIAVHDFRLAERLRPVLRK--- 353 Query: 357 GAARLFD---DVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTM 413 RL D +VD LL P A P LA + MK ++N G+ AL Sbjct: 354 ---RLLDAMSNVDCLLVPGALAPPGPLASVDPFYF-----MKDPIPNIVANYTGFPALAF 405 Query: 414 PVGLDANRMPVGLQLMGPPRAEARLIGIALGIE 446 P G + MPVG+Q+MG PR+E RL+ IA E Sbjct: 406 PAGFGGDGMPVGVQIMGVPRSEHRLLDIAESFE 438 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: 552 Number of extensions: 34 Number of successful extensions: 4 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: 471 Length adjustment: 33 Effective length of query: 429 Effective length of database: 438 Effective search space: 187902 Effective search space used: 187902 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