Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 234 bits (598), Expect = 4e-66 Identities = 158/485 (32%), Positives = 253/485 (52%), Gaps = 17/485 (3%) Query: 15 LSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAIS 74 +SK +PGV A D+V + GEI A+LGENGAGKSTL+K + G D G + G + Sbjct: 14 ISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFNGARAA 73 Query: 75 PKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIG--REPKR-----FGLLRRKEMEKRAT 127 N A+ LGI V+Q +L ++VA+N+ +G R K K++ ++ Sbjct: 74 IHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAGTNMKQLAEQIR 133 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 E YG L+ ++ SV +Q V I RA+ ++LILDEPT+ L Q V+ LF Sbjct: 134 ETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQTLFIT 193 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRE-- 245 +RQL G S+++++H LD++ ++ TV+R G G + + L ++M+G E Sbjct: 194 LRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLMIGGEPP 253 Query: 246 LDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305 + G L+ + ++ +++ +A L++R GEIVG+AG+ G+G+ E Sbjct: 254 REARVQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIAGVSGNGQQELLAA 313 Query: 306 IFGIKPADSGTAL-IKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ 364 + G + A+ + KP Q G+ F PE+R G + S+ NI+L+ Q Sbjct: 314 LSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVPGMSLAANILLSHQ 373 Query: 365 A----QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTR 420 + QRG + P K +A+ I +L ++ + LSGGN QK ++ R + + Sbjct: 374 SAPYVQRGMISP---KAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQKFIVGREIESG 430 Query: 421 PQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQ 480 P+ LI+ +PT G+DVGA A+I + L A G ALLV+S EL+EL DR+ ++ + Sbjct: 431 PKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICDRLHVIAKGRL 490 Query: 481 VAEIP 485 IP Sbjct: 491 SPSIP 495 Lambda K H 0.321 0.138 0.391 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: 575 Number of extensions: 34 Number of successful extensions: 9 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: 500 Length of database: 529 Length adjustment: 35 Effective length of query: 465 Effective length of database: 494 Effective search space: 229710 Effective search space used: 229710 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