Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate WP_011384931.1 AMB_RS12840 thiamine pyrophosphate protein
Query= SwissProt::Q9HUI8 (559 letters) >NCBI__GCF_000009985.1:WP_011384931.1 Length = 561 Score = 164 bits (415), Expect = 9e-45 Identities = 165/520 (31%), Positives = 227/520 (43%), Gaps = 51/520 (9%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGL--PGSGIRHVLTRHEQGAGFMADGYAR 88 T G+ L L G DTV +PG L ++ + RHE GA + A+ + + Sbjct: 10 TGGEILADALLAQGADTVTCVPGESFLPFLDAAWDRRDRLKVLAFRHEGGAAYAAEAHGK 69 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPL-LVISSVNHSASLGKGWGCLHETQDQR 147 ++G+PGVC V GPG T+ + + A+ DS P+ L+I V+ +G E + Sbjct: 70 LTGRPGVCIVGRGPGATHASVGVHTAFQDSTPMVLLIGQVDRPI---RGREAFQEV-ELA 125 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLA--APVAHDWSAA 205 M P+ SP++LPE +ARA+A RP P + +P D+LA A VA D Sbjct: 126 QMFRPLAKRVEEITSPDRLPEAVARAFAAAMGGRPGPAVLILPEDMLAERASVA-DVERL 184 Query: 206 VARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALA--AGEALAALSERLAAPLFTSV 263 P G PC L E LA ARRP+++ GGG A + A +E + P+ Sbjct: 185 PPALPHPG-PC--RLDKMVELLAKARRPLMLVGGGGWTPEAARLITAFAEGWSLPVAACF 241 Query: 264 AGKGLLPPDAPLNAG-ASLCVAPG-WEMIAEADLVLAVGTEMADTDFWRERLPLSGELIR 321 + ++ ++ G +AP + EADL+LAVGT + D D LI Sbjct: 242 RRQDIVDNESACYGGELGYSMAPSLGARVREADLILAVGTRLGDID------TAGYSLIE 295 Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDS---APAAARVARLRAEIRAA 378 + +P A L R L + LP R S APAA +R Sbjct: 296 APNPKQILIHVFPEAEELGRVFRPDLAIVSAMLPFARRASQLAAPAALPWTDWTRAVRGD 355 Query: 379 HAPLQALHQA--------ILDRIAAALPADAFVSTDMTQLAYTGNY-AFASRAPRSWLHP 429 H + + ++ I A LP DA + T GNY + R R +P Sbjct: 356 HLANRVPNSCPGALDMGQVMAEIEARLPEDAIICTG------AGNYTGWPQRFHRFRRYP 409 Query: 430 ----TGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLL 485 G++GYGLPA + AK P R + GDG FL TAQELATA SP VVL+ Sbjct: 410 GQLAPANGSMGYGLPAALAAKALYPDRAVVAFAGDGCFLMTAQELATAKLHGLSP-VVLV 468 Query: 486 WNNDALGQIRDDMLGLDIEPVGVLP---RNPDFALLGRAY 522 +N G IR M P L NPDFA L AY Sbjct: 469 VDNGMYGTIR--MHQEASHPGRTLATDLANPDFAALAAAY 506 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: 860 Number of extensions: 43 Number of successful extensions: 7 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: 561 Length adjustment: 36 Effective length of query: 523 Effective length of database: 525 Effective search space: 274575 Effective search space used: 274575 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