Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_092483295.1 BM299_RS09255 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_900115975.1:WP_092483295.1 Length = 429 Score = 339 bits (869), Expect = 1e-97 Identities = 174/418 (41%), Positives = 271/418 (64%), Gaps = 3/418 (0%) Query: 3 AFILLGSFIVLILIGMPVAYALGLSALIGAWWID-IPLQAMMIQVASGVNKFSLLAIPFF 61 A ILL ++L+L+G P+A++L ++A+ IPL + ++ + + F LLA+PFF Sbjct: 4 ALILLLVLLLLLLVGFPIAFSLAMAAVAALLSKGTIPLTVVPQRLFTATDSFILLAVPFF 63 Query: 62 VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121 VLAG +M GG+SRRLV FA L+G++ GGL+LV+I ++ FF AISGSS A TA++G V+ Sbjct: 64 VLAGELMQHGGISRRLVNFASDLLGWISGGLALVSIASAAFFAAISGSSAATTAAIGGVM 123 Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181 PEM ++GY +F+ V G ++ PPS ++Y + G SI LF+AGI+PGLL Sbjct: 124 YPEMRQRGYKPDFTAVVQAVGGTLGVVIPPSIPLIIYGVITGA--SIGDLFLAGIIPGLL 181 Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241 +AV M + A K Y + L++ EA WGL+ VIILGGI GVFT TE+ Sbjct: 182 GAAVYMAVAWKMAGKLGYKTMQRSSLKKTWHSFREASWGLLMPVIILGGIYGGVFTPTEA 241 Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301 A VAVV++ V FIY++ W++ ++ ++ T +++M+LI A+ F ++MT+ IP Sbjct: 242 AVVAVVYALLVGFFIYKELNWKNFYSMLVKSGLTSAMIMLLIATASLFTWIMTIENIPQA 301 Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361 IT A L++++++ V L+ +N + ++ G +D +IL+L PI P+ +GVDPVHFG+I Sbjct: 302 ITGAILSMTESKLVFLLLVNMVFLIAGMFLDTVAIILLLIPIFFPIALQLGVDPVHFGVI 361 Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 + NL +G +TPP G LFV S + VS+E KA++P+ LA F++++ +TY+P++SL Sbjct: 362 AVFNLAVGQMTPPFGVCLFVSSGVSGVSLEKLFKAVLPYLLAAFILILLLTYVPSLSL 419 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: 3 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: 429 Length adjustment: 32 Effective length of query: 394 Effective length of database: 397 Effective search space: 156418 Effective search space used: 156418 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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