Align ABC transporter for L-Histidine, periplasmic substrate-binding component 2 (characterized)
to candidate YP_004141853.1 Mesci_2668 hypothetical protein
Query= reanno::acidovorax_3H11:Ac3H11_2562 (321 letters) >NCBI__GCF_000185905.1:YP_004141853.1 Length = 335 Score = 120 bits (302), Expect = 4e-32 Identities = 98/316 (31%), Positives = 145/316 (45%), Gaps = 7/316 (2%) Query: 11 LAAAAACVMALAA-PAQAQDTKIVLGMSGWTGFAPLTLADKAGIFKKNGL-DVEI-KMIP 67 LAAA A A AA P + +G+ W G+ +A+ G+FK NGL DV+I Sbjct: 19 LAAAPAAYAADAAIPTTPEAGAFKIGIEPWLGYGQWHVAEAKGLFKTNGLSDVQIVNFAE 78 Query: 68 QKDRHLALASKSIQCAATTVETHVAWNANGVPIVQIFQMDKSYGADGIAVRGDIKSFADL 127 KD + ALAS + A T + A G+P+ + +D S AD I D+ S ADL Sbjct: 79 DKDINAALASGQLDAANIATHTAMGMVAAGLPVKIVLLLDVSMTADAIIAGKDVTSIADL 138 Query: 128 KGKTIGVDAPGTAPYFGLAWMLSKNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEPY 187 KGK + + GT L + L++NGMS+ DVK + A A +AGQ A+TYEPY Sbjct: 139 KGKQVAFEE-GTTSDILLKYALTRNGMSIDDVKPVPMPASDAGSALIAGQVPVAVTYEPY 197 Query: 188 LSTVRDNPAAGKILATTLDYP-MVMDTVGCDPTWLKANGKAAQALANSYFQALDMIKADP 246 L+ K+L T + P ++ D + +K+ A+ S+ AL AD Sbjct: 198 LTVAMAQNKDLKLLFTAGEDPGLISDVLVVRDEVIKSRPGQVLAMIKSWDAALKDYNADT 257 Query: 247 AKSNEIMGAAVKQTGEQFAKSSSFLRWQDKAANQKFFAGELTT-FMKDATAILLEAGIIR 305 I+ AV + + +R+ A N+ G+ TT D A A ++ Sbjct: 258 PGGRAIIAKAVGSDVKDLNTAFDGVRYYSLAENKAALTGDFTTKTFADVEAAAKNAKLL- 316 Query: 306 KANEDLAVTFDASFIK 321 +A+ D SF+K Sbjct: 317 QADVTPEQMIDPSFVK 332 Lambda K H 0.317 0.129 0.374 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: 272 Number of extensions: 19 Number of successful extensions: 3 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: 321 Length of database: 335 Length adjustment: 28 Effective length of query: 293 Effective length of database: 307 Effective search space: 89951 Effective search space used: 89951 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: 49 (23.5 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