Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 189 bits (481), Expect = 8e-53 Identities = 117/302 (38%), Positives = 165/302 (54%), Gaps = 23/302 (7%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M +R++ L K++ G V S I G ++GPSG GKTT LR+IAGLE + Sbjct: 1 MAKVRLDKLRKVYPNGHV---GVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESIS 57 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G + V+ ++P+ R IAMVFQN+ALYP+MTV +N+ F LKL PK +IE Sbjct: 58 GGTLSIGERVVND-----IAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIE 112 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V E + L L L+ P LSGGQ QR A+ RALV+DPKV LLDEP SNLDA++R S Sbjct: 113 RRVAEAARMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLS 172 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R + +I + K T + V+HD + + + V+ G QI TP +Y+ PA +A Sbjct: 173 MRVEIARIHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVA 232 Query: 241 RLTGE--INLIQAKIIENNAIIANLKVPLNN-----------MELKGQSNIVIGLRPDDL 287 G +NL++ + + L +P +E +IV+GLRP+DL Sbjct: 233 GFLGSPAMNLLRGILYRDGG--WKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDL 290 Query: 288 TL 289 L Sbjct: 291 LL 292 Lambda K H 0.317 0.136 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: 294 Number of extensions: 10 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: 371 Length of database: 364 Length adjustment: 30 Effective length of query: 341 Effective length of database: 334 Effective search space: 113894 Effective search space used: 113894 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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