Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate Ga0059261_1585 Ga0059261_1585 Major Facilitator Superfamily
Query= TCDB::Q9A612 (541 letters) >FitnessBrowser__Korea:Ga0059261_1585 Length = 494 Score = 493 bits (1270), Expect = e-144 Identities = 259/501 (51%), Positives = 336/501 (67%), Gaps = 13/501 (2%) Query: 39 MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV 98 M + R F ++N+ FGFFGIQIGF LQNAN SRIFQSLG ++ L LW+AAP TGLLV Sbjct: 1 MEKPRQGFWGLFNLSFGFFGIQIGFALQNANMSRIFQSLGTSIDDLPALWVAAPLTGLLV 60 Query: 99 QPIIGHFSDKTW-GRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINIT 157 QP+IGH SD+TW GR GRRRPYF GAIL LAL MP +P L AA LW++DAS+N++ Sbjct: 61 QPVIGHMSDRTWLGRLGRRRPYFLAGAILAALALFAMPLAPVLLFAAVMLWVLDASLNVS 120 Query: 158 MEPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDS 217 MEPFRAFVGD L +Q + GYA+Q+ FIG GAV S PW L + V+NTAP G +PD+ Sbjct: 121 MEPFRAFVGDMLRKDQHSAGYAVQTAFIGAGAVVGSIFPWALEH-LGVSNTAPGGGIPDT 179 Query: 218 VRIAFYTGGAGLLLAVLWTVFTTREYSPEQLTAFE--KAER-EIAGLGLHEEPEPSVNAY 274 VR AF+ GGA L LAVLWT+ +T+EYSPE++ AF+ +AE E A L S + Sbjct: 180 VRYAFWFGGAALFLAVLWTIVSTKEYSPEEMAAFDGPRAETDETAMRALAARSNTSSLIW 239 Query: 275 IALGVGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFSEV 334 IA G AA+ + V GLEKE+Y+L GLL +G+A + R G N S + Sbjct: 240 IAAG-------AAVIVAVGRFGLEKEVYLLGGLLAGYGVASLIAVLLARRGSGANMLSHI 292 Query: 335 LADVFRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGV 394 + D MP M++LAV QFFSW LF MWI TTP VA + A DA+ Y EGA+WVGV Sbjct: 293 VGDFAGMPPLMKKLAVAQFFSWSALFIMWINTTPVVAQYFYRAADAADSRYQEGANWVGV 352 Query: 395 LFAVYNGVAALAAL-VIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGV 453 LF VYNG+AA+AAL ++PL+ + +H V L GA G SF IRDP L + +G+ Sbjct: 353 LFTVYNGIAAVAALTLLPLLASRIGKARTHIVGLVCGAAGFASFFAIRDPHWLILSEIGI 412 Query: 454 GFAWSSILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIF 513 G AW+SIL+ PY+ILA +LP K+G+YMG+FNVF+VVPQLL AT++G ++K FF ++ I+ Sbjct: 413 GIAWASILAMPYAILASSLPQAKLGIYMGLFNVFVVVPQLLVATVMGSIMKRFFPDEPIW 472 Query: 514 ALVLGALSFALAAAATFLVRD 534 + A++ +AA A V++ Sbjct: 473 TMAFAAVTLLVAAVAMLRVKE 493 Lambda K H 0.327 0.140 0.437 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: 802 Number of extensions: 40 Number of successful extensions: 5 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: 541 Length of database: 494 Length adjustment: 35 Effective length of query: 506 Effective length of database: 459 Effective search space: 232254 Effective search space used: 232254 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: 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