Align Nodulin-26 aquaporin and glycerol facilitator, NIP (de Paula Santos Martins et al. 2015). Transports NH3 5-fold better than water in Hg2+-sensitive fashion (characterized)
to candidate CA265_RS07125 CA265_RS07125 aquaporin Z
Query= TCDB::P08995 (271 letters) >FitnessBrowser__Pedo557:CA265_RS07125 Length = 235 Score = 142 bits (357), Expect = 9e-39 Identities = 83/226 (36%), Positives = 123/226 (54%), Gaps = 15/226 (6%) Query: 37 LQKLVAEAVGTYFLIFAGCASLVV-NENYYNMITFPGIAIVWGLVLTVLVYTVGHISGGH 95 L K AE +GT L+ GC S V+ N + GI+ +GL +T + Y +GHISG H Sbjct: 6 LSKFSAEFLGTLVLVLMGCGSAVIAGANGTTGVGLLGISFAFGLSVTAMAYAIGHISGCH 65 Query: 96 FNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQ-----------F 144 NPA++I R + + Y+VAQ+LG I+ + L + G + F Sbjct: 66 INPAISIGMVIAGRMKIGEAAYYIVAQILGGIVGAFILLQIASGKPEYSLTANGLGQNGF 125 Query: 145 SGTVPNGTNLQA-FVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPV 203 + P +LQA F+ E ++TF + VI G + G FAG+AIG +L L I+G PV Sbjct: 126 AALSPQHYSLQAGFIAEIVLTFIFLLVIFGSTSTKNINGGFAGLAIGLSLTLIHIVGIPV 185 Query: 204 TGASMNPARSLGPAFVHG--EYEGIWIYLLAPVVGAIAGAWVYNIV 247 TG S+NPARS+GPA + G +W++++APV+GA A ++ V Sbjct: 186 TGVSVNPARSIGPALLVGGQALSQVWLFIVAPVIGAALSALIWKTV 231 Lambda K H 0.323 0.138 0.407 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: 202 Number of extensions: 15 Number of successful extensions: 4 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: 271 Length of database: 235 Length adjustment: 24 Effective length of query: 247 Effective length of database: 211 Effective search space: 52117 Effective search space used: 52117 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 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