Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_111606995.1 DK187_RS08910 ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_003259225.1:WP_111606995.1 Length = 394 Score = 213 bits (542), Expect = 7e-60 Identities = 136/372 (36%), Positives = 210/372 (56%), Gaps = 11/372 (2%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M TI + NL+K + G TE +VD VS+T++ G +LGPSG GKTT LR+IAG+E T Sbjct: 1 MPTITLTNLTKCYD-GNTE-PSVDQVSLTVEDGEFMCLLGPSGCGKTTILRMIAGIEHST 58 Query: 61 SGYIYFDNEAVSSPRR-VMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKI 119 SG I D+ V S + + PEKR I +VFQN+AL+P+MTV N+ F L+L KVP + Sbjct: 59 SGEIAVDDLVVDSVHQSCFIPPEKRRIGLVFQNYALWPHMTVERNVDFGLRLQKVPAQER 118 Query: 120 ENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRE 179 + + +V +L + +RYP +LSGGQ QR A+AR L +P VLLLDEP SNLDA +R Sbjct: 119 KERCVDVMSKLRILEYADRYPSQLSGGQQQRVALARMLAVNPGVLLLDEPLSNLDATLRL 178 Query: 180 SARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLI 239 RA +R++ + T + VSHD + +AN V+ G+ QIGTP EIY P+ + Sbjct: 179 EMRAELRRLHQTFGTTIIFVSHDQWEAMTLANTIAVMNKGQLQQIGTPDEIYAEPSNRFV 238 Query: 240 ARLTG--EINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKY 297 A G +INLI+ K E+N + NL + + + V +RP+++ L+DT Sbjct: 239 AEFIGNPKINLIKLK--ESNDELMNLASHILARLPESKFADVCAIRPEEIILTDTANANT 296 Query: 298 IDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIFDL 357 + M I + + + G+ + ++ + ++ + + G + + + + FD Sbjct: 297 LPMNIENI-MPTGGSWVIEL---SLDEDRLFHSTQSRPKWREGEQINAYLPTHSLHFFDH 352 Query: 358 NGSNLITSKTQI 369 + L+ S+T + Sbjct: 353 DEKRLVLSETHL 364 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: 293 Number of extensions: 13 Number of successful extensions: 2 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: 394 Length adjustment: 30 Effective length of query: 341 Effective length of database: 364 Effective search space: 124124 Effective search space used: 124124 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 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