Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3609745 Dshi_3128 ABC transporter related (RefSeq)
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Dino:3609745 Length = 353 Score = 338 bits (866), Expect = 2e-97 Identities = 176/355 (49%), Positives = 231/355 (65%), Gaps = 4/355 (1%) Query: 1 MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60 M+EL+ K VG HI PT LV G NVLLG T GKTSL++LMAGLD G I Sbjct: 1 MIELQEVTKRVGRVTHIKPTSLVFHPGEFNVLLGATGTGKTSLIKLMAGLDPMASGRILM 60 Query: 61 DGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLK 120 G DVT + QKR +++V+Q F+NYP ++V+ NIASP+R++G + I V +AA+LL+ Sbjct: 61 GGQDVTKLNTQKRQISLVHQFFVNYPHMSVFENIASPLRVAGMAKSEIQGRVEEAADLLQ 120 Query: 121 LTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQ 180 L P L R P LSGGQQQRTALARA+ K++ V +DEPLANLDYKLREELRE+LP++FA Sbjct: 121 LRPMLHRKPNELSGGQQQRTALARAIAKDSRAVFLDEPLANLDYKLREELREQLPELFAG 180 Query: 181 SGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTL 240 GA+ VYAT+EP EAL+LGG TA ++ GRVTQFGPT +VYR P NL A +F+DPP+N Sbjct: 181 RGAVVVYATSEPEEALMLGGRTALMDDGRVTQFGPTAQVYREPENLTAARVFSDPPINAA 240 Query: 241 DVTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQAR--TLV 298 ++TK G +G V A +PDG T+A PH + PQ A ++ R LV Sbjct: 241 EITKQGAQIRMQNGAGWEVSGPPAALPDGRYTVAVRPHR--VTPQRSHDAEVELRGTVLV 298 Query: 299 SEITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIA 353 +E++GSES H WV LAHG+H E +++ + FG+DG+ +A Sbjct: 299 TELSGSESSAHFRLGDTDWVSLAHGVHPYKVGEEHVFYMNPENCRYFGTDGKRVA 353 Lambda K H 0.319 0.136 0.392 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: 386 Number of extensions: 12 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: 358 Length of database: 353 Length adjustment: 29 Effective length of query: 329 Effective length of database: 324 Effective search space: 106596 Effective search space used: 106596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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