Align Fructose import permease protein FrcC (characterized)
to candidate Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409 Length = 322 Score = 135 bits (339), Expect = 2e-36 Identities = 89/305 (29%), Positives = 151/305 (49%), Gaps = 15/305 (4%) Query: 52 LIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMV 111 +++ + + +L F S M + ++ GI + + DLSVG+++ Sbjct: 26 MLLAAVGIFVLCTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85 Query: 112 LSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLAS 171 + V+ R L V L +G + G ING ++A++++ I TL QIV Sbjct: 86 CAGVVAA-VVMRDTDSVFLGVSAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGL 144 Query: 172 NFLYSANETIRAQDISANASILQFFGQNFRIGNA-VFTYGVVVMVLLVCLLWY--VLNRT 228 ++++ + + Q F GN +F V +++ +VC L++ +LN T Sbjct: 145 AYIFANGKAVGVSQ-----------EQFFVFGNGQLFGVPVPILITIVCFLFFGWLLNYT 193 Query: 229 AWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFA 288 +GR A+G + EAA LAGVNV R I+ + G+I ALAG L R+ S P GQ Sbjct: 194 TYGRNTMAIGGNQEAALLAGVNVDRTKTLIFAVHGVIGALAGVILASRMTSGQPMIGQGF 253 Query: 289 NIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIA 348 + I+A V+GG+SL GG G I ++ G LI+ + + L D + Y++ G ++++A Sbjct: 254 ELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLA 313 Query: 349 VAIDQ 353 V ID+ Sbjct: 314 VVIDR 318 Lambda K H 0.327 0.141 0.420 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: 321 Number of extensions: 17 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: 360 Length of database: 322 Length adjustment: 28 Effective length of query: 332 Effective length of database: 294 Effective search space: 97608 Effective search space used: 97608 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: 49 (23.5 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