Align Potato X intrinsic protein, XIP1 (characterized)
to candidate Echvi_3097 Echvi_3097 MIP family channel proteins
Query= TCDB::E3UMZ6 (325 letters) >FitnessBrowser__Cola:Echvi_3097 Length = 227 Score = 78.2 bits (191), Expect = 2e-19 Identities = 66/207 (31%), Positives = 93/207 (44%), Gaps = 20/207 (9%) Query: 100 ILIAVVITILLLA--VVPVSGGHINPVISFSAALVGIISMSRAIIYIVAQCLGAVLGALA 157 + +A +T+L +A + VSG H+NP +S G + YI+AQ LG ++ A Sbjct: 38 VALAFGLTVLTMAYAIGHVSGCHLNPAVSIGLWAGGRFEAKELLPYILAQVLGGLVAAAV 97 Query: 158 LRAVVSSSIEDTFSLGGCTVTIIAPGPNGPVTVGLETAQALWLEIFCTFVFLFASIWMAY 217 L + S + F LGG G + P G+ AL E+ TF FLF I A Sbjct: 98 LYVIASDN--PAFELGGFAAN--GYGEHSPGGYGM--TAALVTEVVMTFAFLFV-ILGAT 150 Query: 218 DHRQAKALGHVTVLSIVGLVLGLLVFISTTVTAKKGYGGAGINPARCLGPAIIRGGHLWD 277 + + L V +GL L L+ IS VT +NPAR AI G Sbjct: 151 HSKAPQGLAGVA----IGLCLTLIHLISIPVT------NTSVNPARSTSQAIFVGDWALG 200 Query: 278 GHWIFWVGPTIGCV-AFYVYTKIIPPK 303 W+FWV P +G + A +VY + P K Sbjct: 201 QLWLFWVAPIVGAILAGWVYKYLSPEK 227 Score = 36.2 bits (82), Expect = 8e-07 Identities = 23/86 (26%), Positives = 45/86 (52%), Gaps = 3/86 (3%) Query: 69 LLGSAVLVFMLDTIVISTFESDTKMPNLIMSILIAVVITILLLAVVPVSGGHINPVISFS 128 L+ V+ F +++ S K P + + I + +T++ L +PV+ +NP S S Sbjct: 132 LVTEVVMTFAFLFVILGATHS--KAPQGLAGVAIGLCLTLIHLISIPVTNTSVNPARSTS 189 Query: 129 AAL-VGIISMSRAIIYIVAQCLGAVL 153 A+ VG ++ + ++ VA +GA+L Sbjct: 190 QAIFVGDWALGQLWLFWVAPIVGAIL 215 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: 225 Number of extensions: 17 Number of successful extensions: 3 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: 227 Length adjustment: 25 Effective length of query: 300 Effective length of database: 202 Effective search space: 60600 Effective search space used: 60600 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