Align GlpV, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SMc02514 SMc02514 periplasmic binding ABC transporter protein
Query= TCDB::G3LHZ3 (569 letters) >FitnessBrowser__Smeli:SMc02514 Length = 574 Score = 1119 bits (2895), Expect = 0.0 Identities = 534/567 (94%), Positives = 554/567 (97%) Query: 1 MTTTAGLLLAMTASAYAGMDEAKTFLDKEVGDLSTLPRADQEKEMQWFVDAAKPFAGMDI 60 +TTTA +LLA T SA+AGMDEAK FLDKEVGD+S+L RA QE EMQWFVDAAKPFAGM+I Sbjct: 6 LTTTAAMLLAFTGSAFAGMDEAKQFLDKEVGDMSSLDRAAQEAEMQWFVDAAKPFAGMEI 65 Query: 61 KVVSETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGENIYDAYIND 120 KVVSETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGEN+YDAYIND Sbjct: 66 KVVSETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGENVYDAYIND 125 Query: 121 SDLIGTHWRYQQARSLTDWMANEGKDVTNPGLDIDDFIGKSFTTAPDGKLYQLPDQQFAN 180 SDLIGTHWRYQQARSLTD+MANEGKDVTNP LDIDDFIGKSFTTAPDGKLYQLPDQQFAN Sbjct: 126 SDLIGTHWRYQQARSLTDFMANEGKDVTNPNLDIDDFIGKSFTTAPDGKLYQLPDQQFAN 185 Query: 181 LYWFRYDWFNDEKNKADFKAKYGYDLGVPVNWSAYEDIAEFFTGREIDGKKVFGHMDYGK 240 LYWFRYDWFNDEKNKADFKAKYGY+LGVPVNWSAYEDIAEFFTGREIDGKKV+GHMDYGK Sbjct: 186 LYWFRYDWFNDEKNKADFKAKYGYELGVPVNWSAYEDIAEFFTGREIDGKKVYGHMDYGK 245 Query: 241 KDPSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENSRPVGSCVARGGDTNGPAAV 300 KDPSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENSRPVGSCVARGGDTNGPA+V Sbjct: 246 KDPSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENSRPVGSCVARGGDTNGPASV 305 Query: 301 YSIQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVKEGLPVVNAD 360 Y+IQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVKEGLPVVN D Sbjct: 306 YAIQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVKEGLPVVNED 365 Query: 361 GTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTLMKSTPDDRAKAAWLYAQFVTSKTVDVKK 420 GTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTL+KSTPDDRAKAAWLYAQFVTSKTVDVKK Sbjct: 366 GTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTLLKSTPDDRAKAAWLYAQFVTSKTVDVKK 425 Query: 421 SHMGLTFIRQSTLDHKSFTDRAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQLWWQA 480 SH+GLTFIRQSTLDH+SFT+RAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQLWWQA Sbjct: 426 SHVGLTFIRQSTLDHQSFTERAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQLWWQA 485 Query: 481 IGDASSGAKTAQEAMDSLCSEQEKVLQRLERAKVQGDIGPKLAEEHDLAYWNADAVKNGN 540 IGDASSGAKTAQEAMDSLC+EQEKVLQRLERA VQGDIGPKLAEEHDL YWNA+AVK GN Sbjct: 486 IGDASSGAKTAQEAMDSLCAEQEKVLQRLERAGVQGDIGPKLAEEHDLEYWNAEAVKAGN 545 Query: 541 LAPQLKIENEKDKPVTVNYDELVKSWQ 567 LAPQLK+ENEK+KP TVNYDELVKSWQ Sbjct: 546 LAPQLKVENEKEKPTTVNYDELVKSWQ 572 Lambda K H 0.315 0.132 0.409 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: 1467 Number of extensions: 57 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: 569 Length of database: 574 Length adjustment: 36 Effective length of query: 533 Effective length of database: 538 Effective search space: 286754 Effective search space used: 286754 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 (21.5 bits) S2: 53 (25.0 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