Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_090441639.1 BLS63_RS06690 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_900100495.1:WP_090441639.1 Length = 420 Score = 266 bits (681), Expect = 7e-76 Identities = 143/414 (34%), Positives = 246/414 (59%), Gaps = 11/414 (2%) Query: 10 FIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMI-----QVASGVNKFSLLAIPFFVLA 64 FIVL+ IG+P+A L ++A+ +I + +++ Q G++ + LLAIP F+L Sbjct: 6 FIVLLFIGLPIALVLAVTAMS---YIQLSGNSVLFLSYPQQFFGGLDNYGLLAIPLFMLV 62 Query: 65 GAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPE 124 G +M EGG+++RLVAFA V +G VRGGL+ +NI+A+ +I GS+ A A + V++PE Sbjct: 63 GELMNEGGITKRLVAFASVFLGAVRGGLAYINIIANMMLASIVGSATAQVAVMAQVMVPE 122 Query: 125 MERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSA 184 M KGY R F+TA T +G++ A + PPS V++ + A +SI LF+AGI+PG+L++ Sbjct: 123 MHSKGYDRNFATATTAAGALLAPVIPPSMLFVIFGVLA--QISIGDLFIAGIVPGVLMAG 180 Query: 185 VMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAV 244 + + + YP E + E L +L L V+++G IL GV T TE+AAV Sbjct: 181 GFVAIIALLGFYYQYPASERLSRAEKLNNILRSLPSLSVPVVMIGSILGGVATPTEAAAV 240 Query: 245 AVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKITT 304 + V F + + K+ + ++ R +V+ L+ AA FG+V+ +IP ++ Sbjct: 241 GAAMAVLVGRFAHGEMKFERMGGMLLRVGINSGVVLALVAAAAVFGWVIVYERIPQQLGE 300 Query: 305 AFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGI-GVDPVHFGMIML 363 +++ + ++ ++ + +L+++G V+D +++L PILLPV G+ G++P H G++M Sbjct: 301 VMQSMTSDPFIYMLLVIALLLVVGMVIDGIAALILLVPILLPVAQGVYGINPYHLGVVMC 360 Query: 364 VNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAI 417 +NL +GL+TPPVGA L+V S + ++ L+PF L L+++ + + P + Sbjct: 361 INLTMGLLTPPVGAALYVASRVTGCRPSEIMRPLLPFLLVTLLIMVLIAWQPGL 414 Lambda K H 0.329 0.142 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: 561 Number of extensions: 30 Number of successful extensions: 4 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: 426 Length of database: 420 Length adjustment: 32 Effective length of query: 394 Effective length of database: 388 Effective search space: 152872 Effective search space used: 152872 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 (21.8 bits) S2: 50 (23.9 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