Align L-arabinose isomerase (EC 5.3.1.4) (characterized)
to candidate WP_008539391.1 HMPREF9454_RS09240 L-arabinose isomerase
Query= BRENDA::Q2VMT2 (497 letters) >NCBI__GCF_000245775.1:WP_008539391.1 Length = 494 Score = 573 bits (1477), Expect = e-168 Identities = 284/498 (57%), Positives = 358/498 (71%), Gaps = 10/498 (2%) Query: 2 MLSLRPYEFWFVTGSQHLYGEEALKQVEEHSMMIVNELNQDSVFPFPLVFKSVVTTPEEI 61 M L+ Y+FWF+ GSQ LYG EALK VEE + +V LN P + FK+V TT E I Sbjct: 1 MKKLQDYKFWFIVGSQFLYGPEALKAVEEDAKKMVEGLNASGKLPAKIEFKAVGTTAEVI 60 Query: 62 RRVCLEANASEQCAGVITWMHTFSPAKMWIGGLLELRKPLLHLHTQFNRDIPWDSIDMDF 121 R ++AN + CAG+ITWMHTFSP+KMWI GL +L+KP LHLHTQ+NR+IP + IDMDF Sbjct: 61 DRFVMDANYDDTCAGIITWMHTFSPSKMWIRGLKKLQKPYLHLHTQYNREIPNEEIDMDF 120 Query: 122 MNLNQSAHGDREYGFIGARMGVARKVVVGHWEDPSVRERLAKWMRTAVAFAESRHLKVAR 181 MNLNQSAHGDRE+GFIG RM +ARK+VVG+WE +V+ ++A WMRTA+ S LKV R Sbjct: 121 MNLNQSAHGDREHGFIGTRMRLARKIVVGYWETEAVQNKIATWMRTAIGVIASADLKVIR 180 Query: 182 FGDNMREVAVTEGDKVGAQIQFGWSVNGYGVGDLVQYIRDVSEQKINELLEEYAELYDIV 241 FGDNMR VAVTEGDKV A+I+FGWSVN + VGDLVQYI V+E++I+ + EY Y++ Sbjct: 181 FGDNMRNVAVTEGDKVEAEIKFGWSVNTHAVGDLVQYINAVTEEQIDAQVAEYQTKYEM- 239 Query: 242 PAGRQDGPVRESIREQARIELGLKAFLKDGNFAAFTTTFEDLHGMKQLPGLAVQRLMAEG 301 + S+R QA++E+ +K FL+D F TFEDL+GM QLPGLA Q L +G Sbjct: 240 -----NTDNIASVRYQAKVEVAIKKFLEDNKADGFVNTFEDLYGMDQLPGLATQDLTGQG 294 Query: 302 YGFGGEGDWKTAALVRLMKVMADG--KGTSFMEDYTYHFEPGNE--MILGAHMLEVCPTI 357 YGFG EGDWK A L +MK MA G KGT+ MEDYTYHF E LGAHMLEVCP++ Sbjct: 295 YGFGPEGDWKIACLTAVMKTMAQGVDKGTALMEDYTYHFGKDGEDSYNLGAHMLEVCPSV 354 Query: 358 AATRPRIEVHPLSIGGKEDPARLVFDGGEGAAVNASLIDLGHRFRLIVNEVDAVKPEHDM 417 A P+IEVH L IGGK+ PARLVF+G G A+ A+L+D+G R RLIVN+V+ VKP M Sbjct: 355 AEGTPKIEVHELGIGGKDAPARLVFEGKAGGAIVATLVDMGGRMRLIVNDVECVKPIMPM 414 Query: 418 PKLPVARILWKPRPSLRDSAEAWILAGGAHHTCFSFAVTTEQLQDFAEMAGIECVVINEH 477 P LPVAR++WKP PSL ++ EAWILAGGAHH+ S+ VT EQL+D+A M GIE V I + Sbjct: 415 PNLPVARVMWKPMPSLEEAGEAWILAGGAHHSVISYTVTAEQLRDWANMMGIEFVHITKD 474 Query: 478 TSVSSFKNELRWNEVFWR 495 + FK++L +++ W+ Sbjct: 475 LDMDKFKDQLMLSDIMWK 492 Lambda K H 0.321 0.137 0.423 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: 698 Number of extensions: 31 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: 497 Length of database: 494 Length adjustment: 34 Effective length of query: 463 Effective length of database: 460 Effective search space: 212980 Effective search space used: 212980 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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