Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Pf6N2E2_5839 Glyoxylate carboligase (EC 4.1.1.47)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5839 Length = 588 Score = 177 bits (448), Expect = 1e-48 Identities = 149/494 (30%), Positives = 225/494 (45%), Gaps = 27/494 (5%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPG-SGIRHVLTRHEQGAGFMADGYAR 88 + A +A V ++ GVDT FGIPG LY L GI HVL RH +GA MA+GY R Sbjct: 1 MRAIEAAVLVMRREGVDTAFGIPGAAINPLYSALQKVGGIDHVLARHVEGASHMAEGYTR 60 Query: 89 V-SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 +G GVC +GP T++ T + A ADS+P+L I+ A L K + D Sbjct: 61 TKAGNIGVCIGTSGPAGTDMVTGLYSASADSIPILCITGQAPRARLHKED---FQAVDIT 117 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207 ++ P+T ++ L P Q+P +A+ S RP PV I +P DV A + D A Sbjct: 118 SIVKPVTKWATTVLEPGQVPYAFQKAFFEMRSGRPGPVLIDLPFDVQMAEIEFDIDAYQP 177 Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGAL--AAGEALAALSERLAAPLFTSVAG 265 + + A L A RP+L+AGGG + A E L A +E P+ ++ G Sbjct: 178 LPLAKPAANRVQIEKALAMLNQAERPLLVAGGGIINADASELLVAFAELTGIPVIPTLMG 237 Query: 266 KGLLPPDAPL---NAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGE-LIR 321 G +P D PL G G + ++D+VL +G A+ + G I Sbjct: 238 WGTIPDDHPLMVGMVGLQTSHRYGNATLLKSDVVLGIGNRWANRHTGSVDVYTEGRTFIH 297 Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALL--VRLPQEA-----RDS--APAAARVARLR 372 VDI+P + + + + DA L + R Q A RD+ R A L+ Sbjct: 298 VDIEPTQIGRVFTPDLGIVSDAASALTVFIEVAREWQAAGKLKNRDAWLQDCQQRKASLQ 357 Query: 373 AEIRAAHAPLQALHQAILDRIAAALPAD-AFVST-DMTQLAYTGNYAFASRAPRSWLHPT 430 + + P++ Q + + + D +VST ++Q+A G PR W++ Sbjct: 358 RKTHFDNVPVKP--QRVYEEMNQVFGKDTCYVSTIGLSQIA--GAQFLHVYKPRHWINCG 413 Query: 431 GYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDA 490 G LG+ +PA +G P R + L GD F + +ELA + + P + ++ NN Sbjct: 414 QAGPLGWTIPAALGVVKADPSRKVVALSGDYDFQFMIEELAVGA-QFKLPYIHVVVNNSY 472 Query: 491 LGQIRDDMLGLDIE 504 LG IR G D++ Sbjct: 473 LGLIRQAQRGFDMD 486 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: 703 Number of extensions: 43 Number of successful extensions: 6 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: 588 Length adjustment: 36 Effective length of query: 523 Effective length of database: 552 Effective search space: 288696 Effective search space used: 288696 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