Align D-mannose isomerase (EC 5.3.1.7) (characterized)
to candidate 6936093 Sama_0290 N-acylglucosamine 2-epimerase (RefSeq)
Query= reanno::SB2B:6936372 (389 letters) >FitnessBrowser__SB2B:6936093 Length = 395 Score = 560 bits (1443), Expect = e-164 Identities = 257/389 (66%), Positives = 314/389 (80%), Gaps = 1/389 (0%) Query: 1 MKFYNRDFLLSHSQSILDFYDPRVLDASGGYFHNYYDDGSLFEPGFRQLVSSCRITVNYA 60 M F+++ FLL H QSILDFY RV+D SGGY N+ DDGSLF+ F+QLVSS RI VNYA Sbjct: 1 MNFFSQTFLLEHCQSILDFYTDRVVDPSGGYHQNFLDDGSLFDTHFKQLVSSTRILVNYA 60 Query: 61 RAADILDKPEYLAHARHGLNYLLNVHLQADER-FAWTLKSHRPEDMTQQAYGYAFALLAF 119 A + + +YL ARHGL+YL VH QA + +AWTL +H+P DMTQQAYGYAF LLA+ Sbjct: 61 TAGILFGRQDYLDIARHGLDYLEEVHWQASSQTYAWTLDNHKPLDMTQQAYGYAFVLLAY 120 Query: 120 AACRKSGILKDNNKLLWIYNLLEQRFWQPEYGLYADEIGADGVLSDYRGQNANMHLCEAM 179 AA RK+ +++D++KL +Y+LLEQRFWQ EYGLYADEI +GVLS YRGQNANMHLCEAM Sbjct: 121 AAARKADLVQDDSKLQQVYDLLEQRFWQAEYGLYADEISPEGVLSPYRGQNANMHLCEAM 180 Query: 180 IAAFEASGEGRFLDRAMEIADKIANRQAALTGGIIWEHFTPGFAINWEYNKDDPKNLYRP 239 +AAFEA+G ++L+RA ++A IA RQA+LT ++WEH+TP F +W+YN+DDPKNLYRP Sbjct: 181 LAAFEATGNNQYLERASQLAQSIAVRQASLTNDLVWEHYTPEFKPDWDYNRDDPKNLYRP 240 Query: 240 WGFQGGHQTEWAKLLLSLARHSHQPWLISRAKTLFDTAFEKSWDKEHGGMVYGFGPNGDW 299 WGFQ GHQTEWAKLLL L RH+ Q W I RA +LFD A++++WD + GG+VYGF P G+W Sbjct: 241 WGFQPGHQTEWAKLLLILNRHAPQAWQIERAASLFDRAYQQAWDNQDGGLVYGFDPEGNW 300 Query: 300 CDDDKYFWVQAESFAAAAMLYQQTGEQKYLDAYNALWNYAWQHFVDHEHGAWFRVLYRDN 359 CDDDKYFWVQAESFAAAAML++ TG+ KYL Y+ALW Y+W H VDHE+GAWFRVL +DN Sbjct: 301 CDDDKYFWVQAESFAAAAMLHKATGDDKYLTQYDALWQYSWAHMVDHEYGAWFRVLRKDN 360 Query: 360 RKYSNEKSTAGAKCDYHTLGACFDSLRDL 388 KYSN+KS AGAKCDYHTLGACF+ LR L Sbjct: 361 SKYSNQKSAAGAKCDYHTLGACFEVLRVL 389 Lambda K H 0.322 0.137 0.451 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: 729 Number of extensions: 30 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: 389 Length of database: 395 Length adjustment: 31 Effective length of query: 358 Effective length of database: 364 Effective search space: 130312 Effective search space used: 130312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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