Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 213 bits (542), Expect = 7e-60 Identities = 114/263 (43%), Positives = 170/263 (64%), Gaps = 9/263 (3%) Query: 4 IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63 I EN++K F K + AVDNVS+T++ G F +LGPSG GKTT LR++AG E PT G Sbjct: 15 ITFENVTKRFGK----LAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGR 70 Query: 64 IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123 I D + +S+ + P KR + MVFQ++A++P+MTV DN+A+ LK+ VPK + E +V Sbjct: 71 ILIDGQDISN-----VPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARV 125 Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183 E E + L G+ R P +LSGGQ QR A+ARALVK P+VLLLDEP S LDA++RE R Sbjct: 126 AEALELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRT 185 Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243 + +Q + +T ++V+HD + A+A++ V+ G Q+ TP+++YE+P + +A Sbjct: 186 ELCTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFI 245 Query: 244 GEINLIQAKIIENNAIIANLKVP 266 G++NL + + + A +K P Sbjct: 246 GQVNLFEGVLAVDEPSHAVIKSP 268 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: 313 Number of extensions: 7 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: 381 Length adjustment: 30 Effective length of query: 341 Effective length of database: 351 Effective search space: 119691 Effective search space used: 119691 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