Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate AZOBR_RS23905 AZOBR_RS23905 hypothetical protein
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__azobra:AZOBR_RS23905 Length = 466 Score = 196 bits (498), Expect = 1e-54 Identities = 135/406 (33%), Positives = 196/406 (48%), Gaps = 17/406 (4%) Query: 36 MEPRLNAYKTWDGARARSAAAAVDTLLDQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDE 95 + P +NA D A A A D G G L G+ V+VKD + + G GS + Sbjct: 37 LNPIVNALLAVDADGAIRRARAQDEARAAGDWPGLLDGVTVTVKDCFELAGETTSYGSSD 96 Query: 96 ALPEAWQAAGPLVARLQRQLGIVVGKTHTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGG 155 PL+ RL+ I+VG+ + EF G N H G RNPW RVPGG Sbjct: 97 RFARMGHRDAPLIRRLRDAGAILVGRNNLSEFCLGSTNQNEHHGPCRNPWDTG--RVPGG 154 Query: 156 SSAGAGVSLVQGSALLALGTDTAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTA 215 SS G+ S+ G +++GTDT GS+R+PA++ G VGL+ +VGR G++P S DT Sbjct: 155 SSGGSAASVAAGLCRVSIGTDTGGSIRIPAALCGVVGLRPSVGRVSNSGVIPCSVDFDTV 214 Query: 216 GVLTRTVEDLAYAFAAL------DTESQGLP-----APAPVRVQGLRVGVPTNHFWDDID 264 G L +V D+A AFAA+ D S +P + G R+G+P N ++D++ Sbjct: 215 GPLAYSVADVARAFAAIAGYDPEDPNSVDVPLGNFLPDLKAGIAGTRIGLPRNFYFDNLQ 274 Query: 265 PSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRGGLAASELAAYLDQHFPHKVER 324 P++A V AA L +AGA +V + E A L +++A Y E Sbjct: 275 PAVAERVRAAAAVLEKAGAVLVDVTIEDAEVA-QARTAFSLLVADMAQYHLDKMETAPES 333 Query: 325 LDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIG 384 + P V R++ VS V+Y + L LF+ VD++LTPT + PR+ D Sbjct: 334 IGPEVLRRLQLGLPVSGVQYADSRRWLASWKLRFRALFERVDLILTPTTSITAPRIYDSA 393 Query: 385 TVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMG 430 + A R T G A+++P G D + MPVGLQ++G Sbjct: 394 DM---IEATRAVSRFTYGFGALGLPAMSVPCGFDGDGMPVGLQIVG 436 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: 534 Number of extensions: 27 Number of successful extensions: 5 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: 466 Length adjustment: 33 Effective length of query: 429 Effective length of database: 433 Effective search space: 185757 Effective search space used: 185757 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