Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate HSERO_RS02850 HSERO_RS02850 glutamyl-tRNA(Gln) amidotransferase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__HerbieS:HSERO_RS02850 Length = 651 Score = 150 bits (379), Expect = 1e-40 Identities = 155/504 (30%), Positives = 218/504 (43%), Gaps = 75/504 (14%) Query: 5 HLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQ 64 HL A+ A R R L L A + + P LNA T + +A A +D Q Sbjct: 56 HLQSAQDAGRATSRSLVLAYLARIRA--YDQQGPSLNAIVTLN-PKALEEADQLDRERRQ 112 Query: 65 GQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHT 124 GPL G+P+ VKD Y +P G+ QA V RL+ +++GKT Sbjct: 113 SGPRGPLHGIPILVKDNYDTVDMPTTGGTLALATLQAQADAFQVKRLREAGAVILGKTTM 172 Query: 125 VEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVP 184 E A G V++ G RNP+ P R PGGSS G G ++ A +G+DT GS+R+P Sbjct: 173 HELAAGVTTVSSLTGFTRNPYDPR--RAPGGSSGGTGAAVAASFAAAGMGSDTCGSIRIP 230 Query: 185 ASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAF-AALDTESQ------ 237 A+ GL+TT G G++PLSS+ D A L R+VEDLA A + ++ Q Sbjct: 231 AAHQNLFGLRTTRGLASRSGVMPLSSTQDVAAPLARSVEDLAIMLDATVGSDPQDSSTVD 290 Query: 238 -----------GLPAPAPVRVQGLRVGVPTNHFW-DDIDPSIAAAVEAAVQRLAQAGAQV 285 GL A + +QG R+GV F D ++AA+ A+Q+L GA V Sbjct: 291 ANGHIPKSYRDGLRADS---LQGARIGVLRALFGAAPEDAEVSAAINKALQQLKDQGAIV 347 Query: 286 VRFPLPHCEEAFDIFRRGGLAAS---------ELAAYLDQHFPHKV-------------E 323 +P + G L+ S +L AYL H V E Sbjct: 348 TDVTIPELD--------GLLSGSSIIPYEFKYDLGAYLQSHPGAPVGSLGEILARGMEHE 399 Query: 324 RLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLFDDV------DVLLTPTVPASP 377 L+ +R R Q + K +L+R + L DV D L+ PT+ Sbjct: 400 LLEAGLRLRNSVDLQNPKDKEELEKVMLKR--SALKSLMTDVMQKNHLDTLVYPTIQR-- 455 Query: 378 PRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEAR 437 + A IG + A N +S G AL +PVG + +PV L+L+ P AE Sbjct: 456 -KAALIGEPQGGA-------MNCQLSATTGLPALALPVGFTEDGLPVSLELLAPEFAEPA 507 Query: 438 LIGIALGIEALIGQGHALLGAPDL 461 L+G+A G E IG + P L Sbjct: 508 LLGLAYGWEQKIGPRRSPYSTPAL 531 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: 616 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 462 Length of database: 651 Length adjustment: 36 Effective length of query: 426 Effective length of database: 615 Effective search space: 261990 Effective search space used: 261990 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: 53 (25.0 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