Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate 349724 BT0196 putative hexose phosphate transport protein (NCBI ptt file)
Query= TCDB::Q9Z7N9 (455 letters) >FitnessBrowser__Btheta:349724 Length = 448 Score = 227 bits (579), Expect = 5e-64 Identities = 138/440 (31%), Positives = 221/440 (50%), Gaps = 32/440 (7%) Query: 24 KKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFDKAQLGIIGSTLYFSYGI 83 K++ KY + F S GY YY R S ++ + F + +LGIIGS L+F+Y + Sbjct: 27 KRRLKYLQWSTFLSATFGYGMYYVCRLSLNVVKKPIVDEGIFSETELGIIGSVLFFTYAV 86 Query: 84 SKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGMSSSIVLFALWWGLNGWFQGWGWPPCA 143 KF +G ++D+SN FM GL++T L N+ G S S +LFA+ WG++GWFQ G C Sbjct: 87 GKFTNGFLADRSNINRFMTTGLLVTALINLCLGFSHSFILFAVLWGVSGWFQSMGAASCV 146 Query: 144 RLLTHWYAKSERGTWWSVWSTSHNIGGALIPILTGFIIDYSGWRGAMYVPGILCIGMGLV 203 L+ W+ ERG+++ WS SHNIG AL I+ I+ GWR + G++ + L+ Sbjct: 147 VGLSRWFTDKERGSYYGFWSASHNIGEALTFIIVASIVSVCGWRYGFFGAGMVGLLGALI 206 Query: 204 LINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASEGTEEIERELSTREILFTYVLTNQW 263 + D+P+S G PP+ K + SASE T+ + + VLT Sbjct: 207 VWRFFHDSPESKGFPPVNVPK------EKKTMSASETTDFNKAQ--------RQVLTMPA 252 Query: 264 LWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVKANFCVSLFEIGGLFGMLVAGWLSD 323 +W LA +S F+YI R AVN W +L K Y+ + A+F +S+ + G+ G + +G +SD Sbjct: 253 IWILALSSAFMYISRYAVNSWGVFYLEAQKGYSTLDASFIISISSVCGIIGTMFSGVISD 312 Query: 324 KISKGNRGPMNVLFSLGLLFAILGMWFSRSHNQWWVDGTLLFVIGFFLYGPQMMI----G 379 K+ G R ++F L + A L ++ +W+D + + G G ++I G Sbjct: 313 KLFGGRRNVPALIFGLTNVLA-LCLFLLVPGVHFWLDAVAMILFGL---GIGVLICFLGG 368 Query: 380 LAAAELSHKKAAGTASGFTGWFAYFGATFAGYPLGKV----------TDVWGWKGFFIAL 429 L A +++ + A+G A G G +Y GA G + +V+ + Sbjct: 369 LMAVDIAPRNASGAALGVVGIASYIGAGLQDVMSGVLIEGHKTIRSGVEVYDFTYINWFW 428 Query: 430 LACASIALLLFLPTWNATEK 449 + A +++ L WNA +K Sbjct: 429 IGSAILSVFFALWVWNAKQK 448 Lambda K H 0.327 0.141 0.476 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: 800 Number of extensions: 50 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: 455 Length of database: 448 Length adjustment: 33 Effective length of query: 422 Effective length of database: 415 Effective search space: 175130 Effective search space used: 175130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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