Align Uncharacterized protein (characterized, see rationale)
to candidate WP_024981841.1 BXU11_RS13550 cation:dicarboxylase symporter family transporter
Query= uniprot:A0A0C4Y5S4 (436 letters) >NCBI__GCF_002017945.1:WP_024981841.1 Length = 417 Score = 404 bits (1037), Expect = e-117 Identities = 215/399 (53%), Positives = 281/399 (70%), Gaps = 5/399 (1%) Query: 10 IFIAMLLGVLAGTAAHHYAPDPAAAKSIADHLSILTDVFLRMIKMIIGPLVFATLVSGIA 69 I IAM+LG + G H + +P A+ ++ + IL +F+R+++MII PLVF TLV GIA Sbjct: 19 ILIAMILGAILGIFIHT-SWEPEHAQEFSNKIKILATIFIRLVQMIISPLVFTTLVVGIA 77 Query: 70 SMGDGKAVGRIGMKAMAWFIAASITSLLLGLLMANLLRPGDGMNLALPAADAASNL--KT 127 +GD KAVGRIG KA+AWF AS SLL+G+ N+L PG G+NL+ A A+ + K Sbjct: 78 KLGDVKAVGRIGGKALAWFFTASFISLLIGMFYVNILTPGIGLNLSNIDASTATEVTGKA 137 Query: 128 GALNLREFIAHMFPKSFVEAMATNEILQIVVFSLFFGFALGTLKDGIGKPVLAGIEGLSH 187 +L+ FI H+ PKS +EAMATNEILQIVVFS+FFG A ++ + KP++ ++ LSH Sbjct: 138 QSLSFNNFIEHIVPKSIIEAMATNEILQIVVFSIFFGLAAASIGNH-AKPIVDFMDRLSH 196 Query: 188 VMLKITNYVMAFAPVGVFGAVAAVITAEGLGVLV-VYAKLLGAVYLSLALLWVALIAGGY 246 ++LK+ N+VM FAPVGVFGA+A V L Y K G+ + +A LW+ LIA GY Sbjct: 197 IILKMVNFVMKFAPVGVFGAIAGVFAVRDFSELAFTYFKFFGSFLVGIATLWLILIAIGY 256 Query: 247 FFLGRDVFRLLKMVRAPLMIGFATASSESAYPKVIEQLGRFGVKERITGFVLPLGYSFNL 306 FLG+ + LL + +PL+I F T SSE+ +PK+ E+L RFGVK++I F+LPLGYSFNL Sbjct: 257 LFLGKRMKTLLNHIISPLIIAFGTTSSEAVFPKLTEELERFGVKDKIVSFMLPLGYSFNL 316 Query: 307 DGSIMYTSFAALFVAQVYGIHLSLSQQVTMLLVLLVTSKGIAGVPRASLVVVAAVLPMFG 366 DGS+MY +FA +F+AQ YGI L L Q TMLLVL++TSKGIAGVPRASLVVVAA MF Sbjct: 317 DGSMMYMTFAGIFIAQAYGIDLDLPTQFTMLLVLMLTSKGIAGVPRASLVVVAATCGMFD 376 Query: 367 LPEAGILLVLGIDHVLDMGRTVTNVLGNAIATTVVAKSE 405 +P GI L+L IDH DM R+ TNVLGNA+AT+VV K E Sbjct: 377 IPVEGIALILPIDHFCDMFRSATNVLGNALATSVVGKWE 415 Lambda K H 0.325 0.141 0.401 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: 453 Number of extensions: 22 Number of successful extensions: 6 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: 436 Length of database: 417 Length adjustment: 32 Effective length of query: 404 Effective length of database: 385 Effective search space: 155540 Effective search space used: 155540 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: 51 (24.3 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