Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate GFF360 Psest_0361 TRAP transporter, DctM subunit
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__psRCH2:GFF360 Length = 426 Score = 731 bits (1887), Expect = 0.0 Identities = 369/426 (86%), Positives = 404/426 (94%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60 M+A +LLGSFIVLIL+ +PVAY+LGL+ L+GAWWIDIPL A+MIQ+A GVNKFSLLAIPF Sbjct: 1 MDAVVLLGSFIVLILLRVPVAYSLGLATLVGAWWIDIPLHAVMIQIAGGVNKFSLLAIPF 60 Query: 61 FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120 FVLAGAIMAEGGM+RRLVAFAGVLVGFVRGGLSLVNI ASTFFGAISGSS+ADTASVGSV Sbjct: 61 FVLAGAIMAEGGMARRLVAFAGVLVGFVRGGLSLVNITASTFFGAISGSSLADTASVGSV 120 Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL 180 LIPEME+KGYPREFSTAVT+SGSVQALLTPPSHNSV+YSLAAGGTVSIA+LF+AGI PGL Sbjct: 121 LIPEMEKKGYPREFSTAVTISGSVQALLTPPSHNSVIYSLAAGGTVSIAALFVAGIGPGL 180 Query: 181 LLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATE 240 LLSA M LCL+FA+KRNYPKGEV+PLR+ALKI EALWGLM MVIILGGILSGVFTATE Sbjct: 181 LLSATMATLCLLFARKRNYPKGEVVPLRQALKICVEALWGLMTMVIILGGILSGVFTATE 240 Query: 241 SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPS 300 SAAVAVVW+FFVTMFIYRDYKW +LP+++HRTVRT+SIVMILI FAASFGY+MTLMQIPS Sbjct: 241 SAAVAVVWAFFVTMFIYRDYKWSELPRMLHRTVRTLSIVMILIAFAASFGYIMTLMQIPS 300 Query: 301 KITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGM 360 KITTAFL LSDNRYVILMCINFML++LGT+MDMAPLILILTPILLPV+ GVDPVHFGM Sbjct: 301 KITTAFLALSDNRYVILMCINFMLLVLGTLMDMAPLILILTPILLPVVVSFGVDPVHFGM 360 Query: 361 IMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW 420 IMLVNLGIGLITPPVGAVLFVG+AIGKV+IE+TVKAL+PFY ALF VLMAVTYIP ISLW Sbjct: 361 IMLVNLGIGLITPPVGAVLFVGAAIGKVTIENTVKALLPFYAALFAVLMAVTYIPMISLW 420 Query: 421 LPSVVL 426 LPSVVL Sbjct: 421 LPSVVL 426 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: 760 Number of extensions: 23 Number of successful extensions: 1 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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 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