Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409 Length = 322 Score = 382 bits (981), Expect = e-111 Identities = 190/321 (59%), Positives = 241/321 (75%) Query: 3 SVSTSGSGAPKSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSG 62 +V P+ R D + ML+ +F+ C + + NF + +NM+GLGLAIS +G Sbjct: 2 TVQNKALPTPRKPLDLRRFLDDWVMLLAAVGIFVLCTLLIDNFLSPLNMRGLGLAISTTG 61 Query: 63 MVACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGF 122 + AC ML+CLASG FDLSV SVIACAGV AVV+ T+S+++GV+A L++G++ GL+NG Sbjct: 62 IAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTDSVFLGVSAALVMGLIVGLINGI 121 Query: 123 VIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVA 182 VIAKL++NALITTLATMQIVRGLAYI ++GKAVG+ E FF G FG+P PI +T+ Sbjct: 122 VIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQEQFFVFGNGQLFGVPVPILITIV 181 Query: 183 CLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASR 242 C + FG LLN TT+GRNT+AIGGN+EAA LAGV V RTK +IF + G++ A+AG+ILASR Sbjct: 182 CFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKTLIFAVHGVIGALAGVILASR 241 Query: 243 MTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFA 302 MTSGQPM G+EL VISACVLGGVSL GGIG I +V+AG+LIL +ENAMNL NI F Sbjct: 242 MTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFY 301 Query: 303 QYVVRGLILLAAVIFDRYKQK 323 QYV+RG ILL AV+ DR KQ+ Sbjct: 302 QYVIRGSILLLAVVIDRLKQR 322 Lambda K H 0.327 0.141 0.414 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: 407 Number of extensions: 11 Number of successful extensions: 1 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: 328 Length of database: 322 Length adjustment: 28 Effective length of query: 300 Effective length of database: 294 Effective search space: 88200 Effective search space used: 88200 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: 48 (23.1 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