Align alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (characterized)
to candidate H281DRAFT_03442 H281DRAFT_03442 mannose-6-phosphate isomerase, type 2
Query= CharProtDB::CH_121570 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_03442 Length = 504 Score = 441 bits (1133), Expect = e-128 Identities = 227/478 (47%), Positives = 313/478 (65%), Gaps = 15/478 (3%) Query: 4 VILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERL-----VFEGMDTPIVVCNKD 58 VIL+GGSG+RLWP+SR+QFPKQ + + G+ TL Q T+ R+ ++ + P++VC + Sbjct: 29 VILAGGSGTRLWPVSREQFPKQLIDVIGDKTLLQATMNRMDDFNPLWSVVPDPVIVCGAE 88 Query: 59 HRFIVNEQLANRKLECQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIDDQ 118 H F +EQ + RI++EP R+TAPA+ L A+ +EG D +++ +PADH I D Sbjct: 89 HYFATSEQARESGVNA-RIVVEPGRRDTAPALTLAALTAASEGTDVILVAMPADHAIADL 147 Query: 119 KALQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEKPDE 178 AL +A+ +A A+ G + GVP T P+TG+GYI+ S L +G R+++FVEKP Sbjct: 148 TALHKAIEIAARHADAGAIATLGVPPTGPDTGFGYIRL--GSALSDGAHRIERFVEKPAP 205 Query: 179 KRAVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSEQTADTVTLDDA 238 + A ++V+SG Y+WNSGMF+ RAS +L +++ P I+D CV E ++ T V D Sbjct: 206 ELAAQYVESGNYWWNSGMFVVRASVWLSVIRQFQPQIHDACVRAYEGAKVTDGCVVPDAE 265 Query: 239 TFACCPDNSIDYAVMEKTQR------ACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSKG 292 F P +SIDYAVME + VVPL AGWSD+G W ++W +KD GN S G Sbjct: 266 AFLQSPSDSIDYAVMEHLGKPESPFSGVVVPLEAGWSDLGSWDAVWQAMEKDDCGNASSG 325 Query: 293 DVVIQDSRNCMIHGNG-KLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQGR 351 V+ + + G +L++ +G ++++VVET DA+++A + VQ +K +VS + + Sbjct: 326 RVLFEGATATYARSQGGRLLACVGTNDLIVVETDDAVLVADRSHVQDIKGLVSRIKAEKS 385 Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVT 411 E H +V RPWG YDS+D G RFQVK I V PGA LSLQMHHHRAEHWIVVSGTA VT Sbjct: 386 PEADAHRKVRRPWGFYDSIDQGDRFQVKRIVVMPGARLSLQMHHHRAEHWIVVSGTALVT 445 Query: 412 CDENVFLLTENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRS 469 E FLL EN+STYIP+ HRL NPG +PL+IIEVQSG+YLGEDDI RF+D YGR+ Sbjct: 446 RGEEQFLLGENESTYIPLGIRHRLENPGCVPLQIIEVQSGTYLGEDDIVRFDDKYGRA 503 Lambda K H 0.319 0.135 0.405 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: 694 Number of extensions: 37 Number of successful extensions: 6 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: 483 Length of database: 504 Length adjustment: 34 Effective length of query: 449 Effective length of database: 470 Effective search space: 211030 Effective search space used: 211030 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 (21.8 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