Align Potato X intrinsic protein, XIP1 (characterized)
to candidate CA265_RS07125 CA265_RS07125 aquaporin Z
Query= TCDB::E3UMZ6 (325 letters) >FitnessBrowser__Pedo557:CA265_RS07125 Length = 235 Score = 92.8 bits (229), Expect = 7e-24 Identities = 73/240 (30%), Positives = 110/240 (45%), Gaps = 21/240 (8%) Query: 68 ELLGSAVLVFM-LDTIVISTFESDTKMPNLIMSILIAVVITILLLAVVPVSGGHINPVIS 126 E LG+ VLV M + VI+ T + L +S + +T + A+ +SG HINP IS Sbjct: 12 EFLGTLVLVLMGCGSAVIAGANGTTGVGLLGISFAFGLSVTAMAYAIGHISGCHINPAIS 71 Query: 127 FSAALVGIISMSRAIIYIVAQCLGAVLGALALRAVVSSSIEDTFSLGGCTVTIIAPGPNG 186 + G + + A YIVAQ LG ++GA L + S E + + G G NG Sbjct: 72 IGMVIAGRMKIGEAAYYIVAQILGGIVGAFILLQIASGKPEYSLTANGL-------GQNG 124 Query: 187 PVTVGLE--TAQALWL-EIFCTFVFLFASIWMAYDHRQAKALGHVTVLSIVGLVLGLLVF 243 + + + QA ++ EI TF+FL + + K + +GL L L+ Sbjct: 125 FAALSPQHYSLQAGFIAEIVLTFIFLL----VIFGSTSTKNINGGFAGLAIGLSLTLIHI 180 Query: 244 ISTTVTAKKGYGGAGINPARCLGPAIIRGGHLWDGHWIFWVGPTIGCVAFYVYTKIIPPK 303 + VT G +NPAR +GPA++ GG W+F V P IG + K + K Sbjct: 181 VGIPVT------GVSVNPARSIGPALLVGGQALSQVWLFIVAPVIGAALSALIWKTVLEK 234 Score = 42.7 bits (99), Expect = 9e-09 Identities = 32/126 (25%), Positives = 59/126 (46%), Gaps = 1/126 (0%) Query: 41 KQNFLSLSQRLGIQDFFCLDVWRASMGELLGSAVLVFMLDTIVISTFESDTKMPNLIMSI 100 K + + LG F L S+ + +++ + +VI S + + Sbjct: 110 KPEYSLTANGLGQNGFAALSPQHYSLQAGFIAEIVLTFIFLLVIFGSTSTKNINGGFAGL 169 Query: 101 LIAVVITILLLAVVPVSGGHINPVISFSAAL-VGIISMSRAIIYIVAQCLGAVLGALALR 159 I + +T++ + +PV+G +NP S AL VG ++S+ ++IVA +GA L AL + Sbjct: 170 AIGLSLTLIHIVGIPVTGVSVNPARSIGPALLVGGQALSQVWLFIVAPVIGAALSALIWK 229 Query: 160 AVVSSS 165 V+ S Sbjct: 230 TVLEKS 235 Lambda K H 0.325 0.140 0.430 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: 215 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 325 Length of database: 235 Length adjustment: 25 Effective length of query: 300 Effective length of database: 210 Effective search space: 63000 Effective search space used: 63000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 47 (22.7 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