Align Citrate:H+ symporter (characterized)
to candidate CCNA_01031 CCNA_01031 transporter, major facilitator superfamily
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Caulo:CCNA_01031 Length = 550 Score = 177 bits (449), Expect = 7e-49 Identities = 121/399 (30%), Positives = 195/399 (48%), Gaps = 24/399 (6%) Query: 36 GNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFLMRPIGAIVLGAYIDK 95 G E +DF+L+G A I FF +E ++ F AGF +RP+GA++ G D Sbjct: 24 GTVFEWYDFYLYGSLAPIITSHFFSGVNETTGFILALLAFAAGFAIRPLGALIFGRLGDL 83 Query: 96 VGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQGFSAGAELGGVSVYL 155 GR+ ++T+ +M TF++ L+PSY IG+ AP+ +++ RL+QG + G E GG + Y+ Sbjct: 84 WGRKNTFLITMLLMGVSTFVVGLLPSYAQIGVAAPIALVLMRLVQGLALGGEYGGAATYV 143 Query: 156 AEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISDWGWRIPFLFGVLIVP 215 AE A PG++GFYTSW + + + ++ A+ L A WGWRIPFL +L++ Sbjct: 144 AEHAPPGKRGFYTSWIQTTATIGLFLSLAVILVARIQLGEEAFKAWGWRIPFLVSLLLLG 203 Query: 216 FIFILRRKLEETQEFTAR-RHHLAMRQVFATLLANW---QVVIAGMMMVAM-TTTAFYLI 270 +R KL E+ F ++ NW ++V+ ++ + M +Y Sbjct: 204 VSLWIRLKLHESPTFERMIAEGKGSKKPLTEAFGNWPNLKIVLLALVGLTMGQAVVWYTG 263 Query: 271 TVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLP---VGGALSDRFGRRSVLIAMTLLA 327 YA F +K L L D L LVA++ P + G LSD+ GR+ ++I LLA Sbjct: 264 QFYALFFLEKTLKL---DGALANTLVAVALLIGTPFFVICGWLSDKIGRKPIIILGCLLA 320 Query: 328 LATAWP---ALTMLAN-------APSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEV 377 T +P A+T AN A + +++ + +F + + A ++ A + Sbjct: 321 ALTYFPIFKAITTYANPALAKAEATAPVVVTADTATCAFQFDLIGKAKFNTPCDVAKAYL 380 Query: 378 RVAGFSLAYSLATAVFGGFTPV-ISTALIEYTGDKASPG 415 AG S YS+ A G T V + +E K + G Sbjct: 381 AKAGVS--YSVQAAPAGTPTAVKVGDVTLEGLDSKGATG 417 Score = 48.5 bits (114), Expect = 5e-10 Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 10/109 (9%) Query: 329 ATAWPALT--MLANAPSFLMMLSVL-LWLSFIYGMYNGAMIPALTEIMPAEVRVAGFSLA 385 A +PA L N P+ + +L++L ++++ +YG + L E+ P +R SL Sbjct: 437 AAGYPAKADAALVNKPAVIGLLALLVIYVTMVYG----PIAAMLVELFPTRIRYTAMSLP 492 Query: 386 YSLATAVFGGFTPVISTALIEYTGDKASPGYW--MSFAAICGLLATCYL 432 Y + FGGF P + A++ TGD S G W + AAI ++ +L Sbjct: 493 YHIGNGWFGGFLPTTAFAIVAATGDIYS-GLWYPVIIAAITAVVGGLFL 540 Lambda K H 0.329 0.139 0.421 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: 612 Number of extensions: 33 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 550 Length adjustment: 34 Effective length of query: 410 Effective length of database: 516 Effective search space: 211560 Effective search space used: 211560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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