Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 6938090 Sama_2211 C4-dicarboxylate transport protein (RefSeq)
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__SB2B:6938090 Length = 466 Score = 261 bits (667), Expect = 3e-74 Identities = 156/450 (34%), Positives = 259/450 (57%), Gaps = 38/450 (8%) Query: 9 SFIVLILIGMPVAYALGLSALIGAW-WIDIPLQAMMIQVASGVNK-FSLLAIPFFVLAGA 66 + + +L+GMP+A ALG S+++ + + L ++ +++ ++ ++LLAIPFF+L+ A Sbjct: 9 TLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFFILSSA 68 Query: 67 IMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPEME 126 ++ GG++RR++ FA VG +RGGL++ ++MA F A+SGSS A A++GS++I M Sbjct: 69 FLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMV 128 Query: 127 RKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSAVM 186 R GYP++F+ V + +L PPS ++Y AA VS A +FMAG++PGLL+ ++ Sbjct: 129 RAGYPQKFAAGVITTSGTLGILIPPSIVMLVY--AAATEVSAARMFMAGLIPGLLMGVLL 186 Query: 187 MGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAVAV 246 M I A+ +N P ++ + +A+ GL + I+LG I GV + TE+AAVA Sbjct: 187 MVAIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSIYGGVASPTEAAAVAC 246 Query: 247 VWSFFVTMFIYRDY------KWRD---------LPKLMH------------------RTV 273 V+++ V +F YRD WR + L+H R Sbjct: 247 VYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEIRNVVRDG 306 Query: 274 RTISIVMI-LIGFAASFGYVMTLMQIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMD 332 +SI+++ +I A F +V+T +IP I + + L+ +N +L+ G M+ Sbjct: 307 AKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLLAAGNFME 366 Query: 333 MAPLILILTPILLPVITGIGVDPVHFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIES 392 + ++LI+ PIL P+ +G+DP+H G+IM+VN+ IG++TPPVG LFV + I SI Sbjct: 367 PSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSIGW 426 Query: 393 TVKALMPFYLALFLVLMAVTYIPAISLWLP 422 + A +P+ L L L+ +TY+P ISL+LP Sbjct: 427 VIHACLPWLLLLLGFLVLITYVPQISLFLP 456 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: 29 Number of successful extensions: 5 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: 466 Length adjustment: 32 Effective length of query: 394 Effective length of database: 434 Effective search space: 170996 Effective search space used: 170996 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