Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_101444052.1 BD749_RS08970 amidohydrolase
Query= predicted:W3Y6L2 (394 letters) >NCBI__GCF_002846395.1:WP_101444052.1 Length = 399 Score = 238 bits (608), Expect = 2e-67 Identities = 150/400 (37%), Positives = 210/400 (52%), Gaps = 9/400 (2%) Query: 1 MHTLQDLIKQYASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYK 60 M+ L IK+ A Y V RRHIH+HPELS EE T+A+++ VL G+ + Sbjct: 1 MNQLAQKIKELARAYTHDTVGIRRHIHAHPELSFEEHNTAAYVEQVLQSYGLE-TTRMAA 59 Query: 61 YAVIGEIKGAF-DGPVVGLRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAA 119 V+ IKG + + LRAD+DALPITE + + S+N GVMHACGHD H A LLGAA Sbjct: 60 TGVVALIKGRNPESKTIALRADLDALPITEQNSVDYKSKNEGVMHACGHDVHTASLLGAA 119 Query: 120 AILQSVKDQLHGTVKLVIQPAEEEALIKGAQGIVDSGVLDDVDE--IYGLHVWPQLPVGT 177 ILQ + + GTVKLV QP EE+ GA ++ GVL I G HV+P LP G Sbjct: 120 RILQDLHHEFEGTVKLVFQPGEEK-FPGGASVMIKEGVLQQPAPAGIIGQHVFPMLPAGK 178 Query: 178 VGLKKGNLMAASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNL 237 VG + G MA++D + +KGK H A P +D ++ ++ IV ++ +V+R +P Sbjct: 179 VGFRSGMYMASADEIYITVKGKGGHAALPELNVDPVLITSHLIVALQQVVSRHASPKVPT 238 Query: 238 VCTIGVFNSGDRYNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEY 297 V + G + NV + +EGT RT D R RR+ + L G + ++ Sbjct: 239 VLSFGKVEALGATNVIPNEVKVEGTFRTMDEVWRKEAHRRIRLLAEGLCESMGGSCDIDI 298 Query: 298 RRGHGATINDADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTG 357 + G+ ND D YLG ++VV + M AEDF+ Y ++ F LGT Sbjct: 299 KFGYPFLKNDPDLTGRAREAAALYLGAESVVDLDL-WMGAEDFAYYSQEVAACFYRLGTR 357 Query: 358 FEG---NPALHNAAFTIDESILEPGITMMAGIAAELLQEK 394 + +H F IDE+ LE GI +MA IA + L+ K Sbjct: 358 NDERGITSGVHTPTFDIDEAALETGIGLMAWIAVQELEAK 397 Lambda K H 0.318 0.136 0.401 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: 405 Number of extensions: 15 Number of successful extensions: 5 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: 394 Length of database: 399 Length adjustment: 31 Effective length of query: 363 Effective length of database: 368 Effective search space: 133584 Effective search space used: 133584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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