Align The aerobic dicarboxylate (succinate (Km, 30 μM), fumarate (Km, 79 (characterized)
to candidate WP_086511848.1 BZY95_RS21045 anion transporter
Query= TCDB::A4QAL6 (527 letters) >NCBI__GCF_002151265.1:WP_086511848.1 Length = 532 Score = 456 bits (1172), Expect = e-132 Identities = 242/512 (47%), Positives = 337/512 (65%), Gaps = 51/512 (9%) Query: 36 GLVLAALVYLLFPSNSVETVMQSSGVDPETEYTNNAMRLTAAVTILMAVWWMTEAIPLAA 95 GL++A +V+L + Q+ G+ P+ R A + LMAVWWMTEAIPL+A Sbjct: 34 GLLMALIVWL--------AMGQAEGLSPDA-------RWVATIGTLMAVWWMTEAIPLSA 78 Query: 96 TALIPLVAFPAFQVVDFGKAAAPYANPTIFLFLGGFLMALGLQKWNLHRRMALAVVLAVG 155 TAL+P+V P +A APYA+ +FLFLGGFL+A+ ++KWNLHRR+AL + VG Sbjct: 79 TALLPIVLIPMLTERTVAQATAPYASSIVFLFLGGFLIAIAMEKWNLHRRIALLTLARVG 138 Query: 156 TKPKQLVLGFMVATGFLSMWVSNTATAVVMLPIGMSVLALTAETVG-------------- 201 P ++VLG M+ATGFLSMWVSNTAT ++MLPIG+SVLAL AE G Sbjct: 139 VSPHRIVLGMMLATGFLSMWVSNTATTLMMLPIGLSVLALVAERSGESTETVTADHDHHR 198 Query: 202 -------GMKNQKKFATGLMLSIAYSASIGSLGTLIGTPPNALLAAYMSESHDIHIGFGQ 254 +N K+F L+L+IA+SAS+G LGTL+G+PPNA++A Y ++ +IGF Sbjct: 199 AGHVDFIADENIKRFGLCLLLAIAWSASMGGLGTLLGSPPNAIVAGYAADELGRNIGFLD 258 Query: 255 WMILGVPIAVVFTIIAWLVLTTVFKP-EMKEIPGGRELIKREIAEMGPWTAPQVTVGVIF 313 WM+LGVP+A F ++ W+++T V P +++EIPGG+E+I+ E ++G T + V ++F Sbjct: 259 WMLLGVPLAFTFILVGWVLMTRVLYPFKVEEIPGGQEMIEGEARKLGSLTQGEKMVLLVF 318 Query: 314 AAAALAWVF------IPLTLDWTGSQLSINDSLIGIAAGLLMFIVPANFKTGERILDWRT 367 +AA WV IP W G +++D+ I +AAG+ +F++PA + E +L+W+ Sbjct: 319 GSAAFLWVVPGVLGNIPGVGQWLGPLGNLDDTAIAVAAGIALFVLPARGR-NEMVLNWKD 377 Query: 368 AGE-LPWDVLLLFGGGLSLSAMFTSTGLSLWIGELAKGLDALPIFILIFAIAVLVLFLTE 426 A + LPW VLLLFGGGLSL+ TGL W G+ GL LPI +L+ A+A +VLFLTE Sbjct: 378 AEDGLPWGVLLLFGGGLSLAGAVAGTGLDSWFGQQITGLGVLPILLLVAAVATIVLFLTE 437 Query: 427 FTSNTATAATFLPIMGGVAVGIGLTAGGEQNVLLLTIPVALSATCAFMLPVATPPNAIAF 486 TSNTATAATF+P++GGVAVGIG + + L IP A +ATCAFMLPV TPPNAI F Sbjct: 438 VTSNTATAATFIPVLGGVAVGIGTDS------MTLLIPAAFAATCAFMLPVGTPPNAIVF 491 Query: 487 GSGYIKIGEMVKGGLWLNIIAVILISISTYFV 518 G+G + IG+M +GG+ LNII ++LI++ Y + Sbjct: 492 GTGAVSIGQMARGGVVLNIIGIVLITLFCYLL 523 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: 899 Number of extensions: 57 Number of successful extensions: 9 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: 532 Length adjustment: 35 Effective length of query: 492 Effective length of database: 497 Effective search space: 244524 Effective search space used: 244524 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