Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate AO353_03395 AO353_03395 sugar ABC transporter substrate-binding protein
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03395 Length = 435 Score = 216 bits (551), Expect = 8e-61 Identities = 150/423 (35%), Positives = 212/423 (50%), Gaps = 22/423 (5%) Query: 8 AALGATAALPFGAASATD---LEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGSG 64 A L A P A +A +EV HWWTSGGE AAV L + G W DGA+AG G Sbjct: 14 ATLFPLTAFPLSALAADSKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGG 73 Query: 65 G-TARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRD--LTDIATKENWKEIVKPSS 121 G TA ++ SR G+P Q G +E GL+ L ++ ENW ++ Sbjct: 74 GATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWGSTGLLSTDALKGVSKAENWDGLLS-KK 131 Query: 122 LLDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVE-VPKNWDEFVAAAPALEKAGIVP 180 + D+ EG PVNIH WLW++ A FK+AG++ P +EF AA L+ AG + Sbjct: 132 VSDTVKYEGDYVAVPVNIHRVNWLWINPAVFKKAGIDKAPTTLEEFYAAGDKLKAAGFIA 191 Query: 181 LAVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADD-ARRMSK 239 LA GGQPWQ + F+ +++++ G E ++K D++ +GPE+ K F M Sbjct: 192 LAHGGQPWQDSTVFEDVVLSVMGPEGYKKALVDLDQKTLSGPEMVKSFTELKKLTGYMDP 251 Query: 240 GTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGD 299 +DWN A VI GKAG Q+MGDWA+ E+ A + AG DY C+P G + + D Sbjct: 252 NRAGRDWNIAAADVINGKAGMQMMGDWAKSEWTAAHKVAGKDYQCVPFPGTEKAFTYNID 311 Query: 300 AF-YFPLLEDEEKS-KAQEVLASTLLKPETQVAFNLKKGSLPVRGDV--DLAAA--NDCM 353 + F L D AQ+ LA L + Q F++ KGS+PVR D+ D++AA + C Sbjct: 312 SLAVFKLKADRTGDIAAQQDLAKVALGKDFQKVFSINKGSIPVRTDMLNDMSAAGFDSCA 371 Query: 354 K-KGLDILA--KGNVIQGT---DQLLSADSQKQKEDLFSEFFANHSMTPEDAQKRFADII 407 + D LA K +Q + + S Q D+ + F + S P A + A I Sbjct: 372 QASAKDFLADEKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKSADPAKASAQLASAI 431 Query: 408 AAA 410 AA Sbjct: 432 KAA 434 Lambda K H 0.315 0.131 0.389 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: 525 Number of extensions: 30 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: 411 Length of database: 435 Length adjustment: 32 Effective length of query: 379 Effective length of database: 403 Effective search space: 152737 Effective search space used: 152737 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 (21.6 bits) S2: 50 (23.9 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