Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate WP_089216658.1 CHB69_RS14150 MFS transporter
Query= TCDB::Q9A612 (541 letters) >NCBI__GCF_900188185.1:WP_089216658.1 Length = 499 Score = 483 bits (1244), Expect = e-141 Identities = 248/493 (50%), Positives = 330/493 (66%), Gaps = 9/493 (1%) Query: 39 MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV 98 M + R F +WN+ FGFFGIQIGF LQNAN SRIFQSLG D+ L LW+AAP TGLLV Sbjct: 1 MEKPRQGFAGLWNISFGFFGIQIGFALQNANMSRIFQSLGEDIEKLPGLWVAAPLTGLLV 60 Query: 99 QPIIGHFSDKTW-GRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINIT 157 QP+IGH SD+TW GR GRRRPYF GAIL +AL MP SP++W AA LW++DAS+NI+ Sbjct: 61 QPVIGHLSDRTWLGRLGRRRPYFLAGAILAAIALFAMPESPSIWFAAVMLWLLDASLNIS 120 Query: 158 MEPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDS 217 MEPFRAFVGD L +Q + GYA+Q+ FIG GAV S P ++ F VAN AP GQ+P++ Sbjct: 121 MEPFRAFVGDMLRKDQHSAGYAVQTAFIGAGAVVGSLFPSVMEA-FGVANVAPPGQIPET 179 Query: 218 VRIAFYTGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAY-IA 276 VR AF+ GGA LLL+VLWTV +T EY P ++ AFE A G + P ++ ++ A Sbjct: 180 VRYAFWFGGAALLLSVLWTVVSTDEYDPARMAAFETA-----GDAVELPPMRALASHSYA 234 Query: 277 LGVGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFSEVLA 336 G + G +AL+ GL +E+ +L LL +GLA + R G + N S ++ Sbjct: 235 ASFGWIAAGVVVALVQIRLGLLREVLLLGALLAGYGLASMLAIALARRGSSTNMLSSIVG 294 Query: 337 DVFRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLF 396 D MP M++LA+VQFFSW LF MWI TTP VA H+G DA+S AY E A+WVG LF Sbjct: 295 DFSGMPALMKRLAIVQFFSWSALFVMWINTTPIVAQYHYGTRDAASAAYQEAANWVGELF 354 Query: 397 AVYNGVAALAAL-VIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGF 455 A+YNGVAA+AAL ++P + + + +H L GA G SF V+RDP L + + +G Sbjct: 355 AIYNGVAAIAALTLLPWLARRLGQARTHMTGLACGAAGYASFFVLRDPMHLIVSEIFIGI 414 Query: 456 AWSSILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFAL 515 W+S+L+ PY+ILA +LP K+GVYMG+FNVF+V+PQLL AT++G +++ FF + I+ + Sbjct: 415 FWASVLAMPYAILASSLPQAKLGVYMGLFNVFVVIPQLLVATVMGSVMQAFFPGEPIYTM 474 Query: 516 VLGALSFALAAAA 528 A++ +A A Sbjct: 475 AFAAVTLMVAMIA 487 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: 770 Number of extensions: 37 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: 499 Length adjustment: 35 Effective length of query: 506 Effective length of database: 464 Effective search space: 234784 Effective search space used: 234784 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 24 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