Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 3610459 Dshi_3840 thiamine pyrophosphate protein TPP binding domain protein (RefSeq)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Dino:3610459 Length = 546 Score = 176 bits (446), Expect = 2e-48 Identities = 160/540 (29%), Positives = 231/540 (42%), Gaps = 33/540 (6%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 + QALV L + GVDTV+G+PG T L L S + VL RHEQ A FMA + R++ Sbjct: 6 SGAQALVESLFSAGVDTVYGVPGEETTALMAALHDSEMAFVLCRHEQAAAFMAGVHGRLT 65 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150 G+P C GPG TN+ T + A D VP++ I+ LG+ H+ D A+ Sbjct: 66 GRPAACLATLGPGATNLVTGVADATLDFVPMIAITGQGGCGRLGRE---SHQIIDLEALF 122 Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRP 210 AP+T S L + +P +A A + +E+P VH+ +P DV A A P Sbjct: 123 APVTKQSRTLLEADAVPGAVAEAVRLARAEKPGAVHLCLPEDVADAQTALRDVPVPQVLP 182 Query: 211 GRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEA--LAALSERLAAPLFTSVAGKGL 268 P EA+ A L A RP+L+AG G + AG L A +E + TS G+ Sbjct: 183 --SPPAPEAIAQALTLLTRAERPILLAGAGVIRAGATAELRAFAEATGIAVVTSFMAGGV 240 Query: 269 LPPDAPLNAGASLCVAPGWEMI----AEADLVLAVG---TEMADTDFWRE-RLPLSGELI 320 LPP+ L P + + ADL+++VG E D R+ +P ++ Sbjct: 241 LPPEHELT--LFTVGQPEGDYVDLSFEAADLIVSVGFDPVEYPAADLSRDGAIP----VL 294 Query: 321 RVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAA------RVARLRAE 374 + P + + A + +TL AL L D PA A R A RA Sbjct: 295 HLGAGPAPADAGWHVAGQVVAGLPETLAALAEALEARRWDMPPAFAGVQAGMRKAFARAY 354 Query: 375 IRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGT 434 ++ P+ Q I I L A+ V + + R P + P G Sbjct: 355 STSSEGPVAP--QDICAEITRQLRAEDTVLSGVGLHKLWIARHVLPRRPGQVIIPNGLAG 412 Query: 435 LGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQI 494 +G LP + A L + GDG + Q++ TA+ L L V++W + G I Sbjct: 413 MGLALPGAVAAARLQQAGRVLAICGDGDVMMNVQDMETAA-RLGLDLTVMVWEDGGYGLI 471 Query: 495 -RDDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 D G PD+ L RA+G + L EL LRAG +G TL+ + Sbjct: 472 DAHQQKAGDDSTFGF--GTPDWGRLARAFGWSHAPVAGLSELGEILRAGHDSAGPTLVSV 529 Lambda K H 0.321 0.136 0.412 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: 862 Number of extensions: 49 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: 559 Length of database: 546 Length adjustment: 36 Effective length of query: 523 Effective length of database: 510 Effective search space: 266730 Effective search space used: 266730 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