Align MalE aka PF1739, component of Maltose/trehalose porter (characterized)
to candidate Synpcc7942_0950 Synpcc7942_0950 putative multiple sugar transport system substrate-binding protein
Query= TCDB::O51923 (450 letters) >FitnessBrowser__SynE:Synpcc7942_0950 Length = 438 Score = 210 bits (535), Expect = 6e-59 Identities = 139/421 (33%), Positives = 231/421 (54%), Gaps = 20/421 (4%) Query: 26 IGGQQTSTVTSTPTETSLQGKIVFAVGGAPNEIEYWKGVIAEFEKKYPGVTVELKRQATD 85 +GG T T S ++++ ++ A+ AP E + IA F ++P + +EL D Sbjct: 29 LGGLGTGTQRSAAADSTV---VLRALLPAPFR-EAMQPAIARFTAEHPEIQLELVAGPND 84 Query: 86 TEQRRLDLVNALRGKSSDPDVFLMDVAWLGQFIASGWLEPLDDYVQKDNYDLSVFFQSVI 145 T A ++ D+ +DV WL +F+A+GWL L D V + + F + + Sbjct: 85 TSLVSDLYTTAFLLGNAPYDLVFLDVTWLPKFVAAGWLLDLSDRVLPEIQ--AEFLPAAL 142 Query: 146 NLADKQGGKLYALPVYIDAGLLYYRKDLLEKYGYSKPPETWQELVEMAQKIQSGERETNP 205 N +LY LP+ GLLYYR+DL+ + PP+T+ ELV+ +Q++Q+ + P Sbjct: 143 N-GSFYRDRLYRLPLNAAVGLLYYRQDLMPE-----PPQTFTELVQRSQQLQA--QGVVP 194 Query: 206 NFWGFVWQGKQYEGLVCDFVEYVYSNGGSLGEFKDGKWVPTLNKPENVEALQFMVDLIHK 265 WG+VWQGKQYEGLVC+F+E + GG + + G+ L+ PE + A ++ I Sbjct: 195 --WGYVWQGKQYEGLVCNFLEVLAGFGGYWIDPQTGE--VGLDHPEAIAAADWLHSTITD 250 Query: 266 YKISPPNTYTEMTEEPVRLMFQQGNAAFERNWPYAWGLHNADDSPVKGKVGVAPLPHFPG 325 +ISP T E ++L F+ G +AF RNWPYA L +S V+GKVG+AP+ H PG Sbjct: 251 -QISPAGVSTFQENEALKL-FETGQSAFMRNWPYAEMLLERPESAVRGKVGIAPMVHAPG 308 Query: 326 HKSAATLGGWHIGISKYSDNKALAWEFVKFVESYSVQKGFAMNLGWNPGRVDVYDDPAVV 385 SAAT G W +GI++ +++ A + + Q+ ++ + P R +Y DP ++ Sbjct: 309 QTSAATQGTWGVGIAQQTEHPEAALTALLALTDAESQRLISLGSNYIPTRSALYQDPELL 368 Query: 386 SKSPHLKELRAVFENAVPRPIVPYYPQLSEIIQKYVNSALAGKISPQEALDKAQKEAEEL 445 ++ P L + E+ V R +P Y LS+I+Q+++++A++G+ AL +A +E+ +L Sbjct: 369 ARYPFYATLPPILESTVLRSPLPAYDALSDILQRHLSAAISGQTPVAIALQQAARESRQL 428 Query: 446 V 446 + Sbjct: 429 L 429 Lambda K H 0.316 0.136 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: 452 Number of extensions: 26 Number of successful extensions: 6 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: 450 Length of database: 438 Length adjustment: 32 Effective length of query: 418 Effective length of database: 406 Effective search space: 169708 Effective search space used: 169708 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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