Align The aerobic dicarboxylate (succinate (Km, 30 μM), fumarate (Km, 79 (characterized)
to candidate WP_084609424.1 Q385_RS0108670 anion transporter
Query= TCDB::A4QAL6 (527 letters) >NCBI__GCF_000619805.1:WP_084609424.1 Length = 460 Score = 246 bits (629), Expect = 1e-69 Identities = 145/451 (32%), Positives = 254/451 (56%), Gaps = 26/451 (5%) Query: 73 RLTAAVTILMAVWWMTEAIPLAATALIPLVAFPAFQVVDFGKAAAPYANPTIFLFLGGFL 132 ++ + +L WW+ E +P+ T L L+ + +VD K ++NP I L +G FL Sbjct: 16 KVVLGILLLCIFWWLFEVVPVGITGLFGLILAVFYGIVDVDKVFIGFSNPVILLMIGSFL 75 Query: 133 MALGLQKWNLHRRMALAVVLA--VGTKPKQLVLGFMVATGFLSMWVSNTATAVVMLPIGM 190 +A + K+ L +R++L ++ P ++++GF + T LSMW+SNTAT +MLPI + Sbjct: 76 IAHSVNKYGLDKRISLNILSKDFFIKSPIRVIIGFSLITFLLSMWLSNTATTAMMLPIVL 135 Query: 191 SVL-ALTAETVGGMKNQKKFATGLMLSIAYSASIGSLGTLIGTPPNALLAAYMSESHDIH 249 V+ L E + G KN FA+ ++LSIAYSASIG +GT++G+P N + ++ E I Sbjct: 136 GVIYLLKEEKIQGYKN---FASFMLLSIAYSASIGGIGTIVGSPTNLVGLGFLKEE-GIS 191 Query: 250 IGFGQWMILGVPIAVVFTIIAWLVLTTVFKPEMKEIPGGRELIKREIAEMGPWTAPQVTV 309 I F QW++L +PIA+ +I L + + + ++++E ++ + + + Sbjct: 192 IDFFQWILLMLPIALSMYVIMILYIRFFLRKVKFNPQEIKTILQKEKEKLPKMSKEEKII 251 Query: 310 GVIFAAAALAWVFIP----LTLDWTGSQLS--INDSLIGIAAGLLMFIVPANFKTGERIL 363 +F A W+F + + G Q+S I +S++ + + L+F++P + K + IL Sbjct: 252 AGVFLLAVFLWIFPSFIGIIGFEELGKQISKKIPESIVAVLSAGLLFLIPKDLKNYQTIL 311 Query: 364 DWRTAGELPWDVLLLFGGGLSLSAMFTSTGLSLWIGEL-AKGLDALPIFI--LIFAIAVL 420 E+ W+ ++LF G+S+ + +S+GL GE+ AK L ++ L+F + V+ Sbjct: 312 TVEDLKEVDWNTVILFASGISIGKLISSSGL----GEIIAKSLSGYITYVPLLLFILIVV 367 Query: 421 VLFLTEFTSNTATAATFLPIMGGVAVGIGLTAGGEQNVLLLTIPVALSATCAFMLPVATP 480 ++ LTE SNTAT TF PI+ I L + + + T+ + ++++ AFM P+ATP Sbjct: 368 IILLTEINSNTATVITFAPII------IALLKNNQIDFVYPTLAIIVASSFAFMFPIATP 421 Query: 481 PNAIAFGSGYIKIGEMVKGGLWLNIIAVILI 511 PNAI + +G+IK+ +M K GL+LN + I+I Sbjct: 422 PNAIVYSTGFIKLQDMAKFGLFLNAVGSIVI 452 Lambda K H 0.324 0.139 0.418 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: 620 Number of extensions: 33 Number of successful extensions: 8 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: 527 Length of database: 460 Length adjustment: 34 Effective length of query: 493 Effective length of database: 426 Effective search space: 210018 Effective search space used: 210018 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 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