Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate HSERO_RS05555 HSERO_RS05555 ABC transporter permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__HerbieS:HSERO_RS05555 Length = 618 Score = 211 bits (537), Expect = 5e-59 Identities = 126/415 (30%), Positives = 226/415 (54%), Gaps = 16/415 (3%) Query: 12 VLILIGMPVAYALGLSALIGAWWIDI---PLQAMMIQVASGVNKFSLLAIPFFVLAGAIM 68 V +L+G+P+A+ GL+ + A+ + + PL + + G++ LLA+P F+L G ++ Sbjct: 210 VSVLLGIPIAFCFGLATV--AFMLTVTTSPLAVVAGRFDEGMSSLILLAVPLFILLGHLV 267 Query: 69 AEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPEMERK 128 GM++ +V F L+G VRGGL+ V + A ISG+ AD A+V VL+PEM+R+ Sbjct: 268 EMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPVLLPEMKRR 327 Query: 129 G-YPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSAVMM 187 G + E + + SG++ + P + VL ++ + VSIA+LF GIMPG++L+ ++ Sbjct: 328 GNHEGELISLLAASGAMAETIPP---SLVLITIGSVAGVSIAALFTGGIMPGIVLAVLLA 384 Query: 188 GLCLIFAKKRNYPKGEVI---PLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAV 244 I A+ R+ E I P R L+ AL L+ ++I ++ GV TATE + + Sbjct: 385 ----ILARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATATEVSTI 440 Query: 245 AVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKITT 304 + +S + +YR + W+ L ++ T ++ +IG A + +T + Sbjct: 441 GIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFSHALAE 500 Query: 305 AFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIMLV 364 A ++ +Y L+ ++LG+V++ P +++ P+L PV IGV VH+ M++++ Sbjct: 501 AMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYAMVIIL 560 Query: 365 NLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419 ++G+GL PP G + IG+V + VK + P+ AL + L+ V ++P S+ Sbjct: 561 SMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI 615 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: 759 Number of extensions: 47 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: 618 Length adjustment: 35 Effective length of query: 391 Effective length of database: 583 Effective search space: 227953 Effective search space used: 227953 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: 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