Align Alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate Pf6N2E2_1643 Trehalase (EC 3.2.1.28); Periplasmic trehalase precursor (EC 3.2.1.28)
Query= reanno::pseudo5_N2C3_1:AO356_24205 (541 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1643 Length = 547 Score = 1035 bits (2675), Expect = 0.0 Identities = 497/539 (92%), Positives = 511/539 (94%) Query: 1 MRPIELTSLSFATLLCVACSSQPPATWSYVDAQGRANLPPDQAYPELFEAVQRGQVFTDQ 60 MRP+ TSLSFA LLCVACSSQPPATWSY DAQGRANLPPDQ YPELFEAVQR QVFTDQ Sbjct: 6 MRPLYFTSLSFAALLCVACSSQPPATWSYADAQGRANLPPDQTYPELFEAVQREQVFTDQ 65 Query: 61 KHFVDALPNRDPAQIRADYLARRDHDGFDIKAFVKDNFIESGQAESPAPKPGAPIQEHID 120 KHFVDALPNRDPAQIRADYL RR+ DGFDIKAFVKDNFIESG+ ESPAPKPGAPI+EHID Sbjct: 66 KHFVDALPNRDPAQIRADYLDRRNRDGFDIKAFVKDNFIESGEVESPAPKPGAPIKEHID 125 Query: 121 SLWPILSRSYSQVPAYSSLLPLPQPYVVPGGRFREMYYWDSYFTMLGLEQSGDKARVRQM 180 SLWP+LSRSY QVPAYSSLLPLPQPYVVPGGRFREMYYWDSYFTMLGLEQSGD+A+VRQM Sbjct: 126 SLWPVLSRSYRQVPAYSSLLPLPQPYVVPGGRFREMYYWDSYFTMLGLEQSGDEAQVRQM 185 Query: 181 TDNFAYMIDTYGHIPNGNRTYYLSRSQPPFFAYMVALQARIEGDQAYGRYLPQLQKEYAY 240 TDNFAYMIDTYGHIPNGNRTYYLSRSQPPFFAYMV LQARIEGDQAYGRYLPQLQKEYAY Sbjct: 186 TDNFAYMIDTYGHIPNGNRTYYLSRSQPPFFAYMVELQARIEGDQAYGRYLPQLQKEYAY 245 Query: 241 WMAGAQALKPGAADRHVVKLADGSVLNRYWDASPTPRQESWLQDVRTAEQAPDRPKEEVW 300 WM GAQ+LKPG+A RHVVKLADGSVLNRYWDASPTPRQESWLQDV TAE+APDRPKEEVW Sbjct: 246 WMEGAQSLKPGSAARHVVKLADGSVLNRYWDASPTPRQESWLQDVSTAERAPDRPKEEVW 305 Query: 301 RDLRAGAESGWDFSSRWLDDGQNLASIRTTAIVPVDLNSLIYHLEQTIAKACETVQNAPC 360 RDLRAGAESGWDFSSRWLDDGQNLASIRTTAIVPVDLNSLIYHLE TIAKACETVQN PC Sbjct: 306 RDLRAGAESGWDFSSRWLDDGQNLASIRTTAIVPVDLNSLIYHLENTIAKACETVQNIPC 365 Query: 361 VQAYGRRAELRQRAIEQHLWNADKGFYVDYDWQRQQQRQQLTAATLFPLYTGLASAEHAH 420 VQAYGRRAELRQRAIE+HLWNADKGFYVDYDWQR Q RQ LTAATLFPLYTGLAS EHA+ Sbjct: 366 VQAYGRRAELRQRAIEKHLWNADKGFYVDYDWQRNQPRQPLTAATLFPLYTGLASVEHAN 425 Query: 421 RTADAVRDGLLRVAGIATTQVNTGQQWDEPNGWAPLQWVAVEGLDRYGHTALAQQVGSRF 480 RTADAVRDGLLR GIATTQV+ GQQWDEPNGWAPLQWVAVEGLDRY TALAQQ+GSRF Sbjct: 426 RTADAVRDGLLRPGGIATTQVSNGQQWDEPNGWAPLQWVAVEGLDRYQQTALAQQIGSRF 485 Query: 481 LQQVENLYRKENKLVEKYDLSGRGDGGGGGEYELQDGFGWTNGVTLKLLGKYGKTSSTL 539 LQQVENLYRKENKLVEKYDLSGRGDGGGGGEYELQDGFGWTNGVTLKLLGKYG T TL Sbjct: 486 LQQVENLYRKENKLVEKYDLSGRGDGGGGGEYELQDGFGWTNGVTLKLLGKYGATPPTL 544 Lambda K H 0.318 0.134 0.418 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: 1177 Number of extensions: 48 Number of successful extensions: 1 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: 541 Length of database: 547 Length adjustment: 35 Effective length of query: 506 Effective length of database: 512 Effective search space: 259072 Effective search space used: 259072 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 (21.7 bits) S2: 52 (24.6 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