Align The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__ANA3:7025672 Length = 452 Score = 187 bits (475), Expect = 7e-52 Identities = 160/523 (30%), Positives = 253/523 (48%), Gaps = 77/523 (14%) Query: 23 MPAAGLMISIGKLIGMSAGDINAVHTIARV-MEDIGWAIITNLHILFAVAIGGSWAKDRA 81 MPAAG+M+ G++ I + + V M +G I + ILFAVA+ + +D+ Sbjct: 1 MPAAGVML------GLTVSPIPFMPEVLTVLMLAVGKLIFAIMPILFAVAVAIGFCRDQG 54 Query: 82 GGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIVKDYFTSVLGAPALNM 141 AF A+ + + A LAD + +L LG L+ Sbjct: 55 IAAFTAVFGYGVMTATLAA--------LADLYQLPTQLL-------------LGMETLDT 93 Query: 142 GVFVGIITGFLGATLYN-KYYNYNKLPQALAFFNGKRFVPFVVIVWSTVTAIVLSLLWPF 200 G+ G++ G G T + ++ Y +LP +FF G+R ++I + +L+ +WP Sbjct: 94 GIAGGMLIG--GVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYILAHVWPP 151 Query: 201 IQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPMNYTELGGTYTMLT 260 + + W K P +A VYG LERLL+P GLHH+ P Y E+G Y + Sbjct: 152 LSLLIERVSDWAVYQK---PAIAFGVYGALERLLIPLGLHHIWNAPF-YLEVG-QYQLQN 206 Query: 261 GSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFKAGQVIGSTAALMG 320 +VV G+ +LA GD +A N AG + L Sbjct: 207 S----EVVRGEVARYLA-----------GDPQAGN-----------LAGGYLIKMWGLPA 240 Query: 321 IAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPVLYVVYAITTGLAF 380 A A++R + +R + + LSAA A +LTGVTEPIEF FMF+AP L++++ + +GLA+ Sbjct: 241 AALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPFLFLIHVLLSGLAY 300 Query: 381 ALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSLVFFGLNFTLFNFLIKKFN 440 + ++++ H+ F + ++ + L+R+ FV + + + + LF I FN Sbjct: 301 FVCIMLDIH-HSIVFSHGLVDFTLLFS--LSRNTGWFVFLGPLTAVIYYLLFRGSILAFN 357 Query: 441 LPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIADVDACMTRLRVTVKDL 500 L TPGR E E G + +I LGG+ENI +++AC+TRLR++V Sbjct: 358 LKTPGRL--------EPDEPHGAKES---LRAIIAALGGRENIVELNACLTRLRLSVHSP 406 Query: 501 DVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQDML 543 ++V + + Q GA G+IV KGVQ VYG KA+ L+ +Q L Sbjct: 407 ELV-NKVRLSQLGAKGVIVMGKGVQVVYGTKAETLRKVLQRYL 448 Lambda K H 0.325 0.140 0.416 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: 581 Number of extensions: 30 Number of successful extensions: 7 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: 545 Length of database: 452 Length adjustment: 34 Effective length of query: 511 Effective length of database: 418 Effective search space: 213598 Effective search space used: 213598 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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