Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 17640 b3579 predicted transporter (NCBI)
Query= SwissProt::Q9KQR9 (332 letters) >FitnessBrowser__Keio:17640 Length = 328 Score = 141 bits (355), Expect = 3e-38 Identities = 102/328 (31%), Positives = 166/328 (50%), Gaps = 23/328 (7%) Query: 7 LIAASILAVTSFNAAANCDPGEIVIKFSHVTN-TDKHPKGIAASLLEKRVNEEMNGKACM 65 L A + A ++ + AA ++F + T+ TD + IAA + E G+ + Sbjct: 10 LFIAGLAAFSTSSLAAQS------LRFGYETSQTDS--QHIAAKKFNDLLQERTKGELKL 61 Query: 66 QVFPNSTLYDDDKVLEALLNGDVQLAAPSLSKFEKFTKKYRIFDLPFLFEDVDAVDRFQS 125 ++FP+STL + ++ + G + + + F + + D+PFLF D + Sbjct: 62 KLFPDSTLGNAQAMISGVRGGTIDMEMSGSNNFAGLSPVMNLLDVPFLFRDTAHAHKTLD 121 Query: 126 SAKGEELKNAMTRRGVKGLEFWHNGMKQISANK-PILVPADAKGLKFRVQASDVLVAQFE 184 G++LK ++ +G+K L +W NG + ++ ++ P+ PAD KGLK R S + +A F+ Sbjct: 122 GKVGDDLKASLEGKGLKVLAYWENGWRDVTNSRAPVKTPADLKGLKIRTNNSPMNIAAFK 181 Query: 185 QIGANPQKMSFAETYGGLQTKVIDGQENTWSNIYGQKYFEVQDGTTETNHGILDYLVVTS 244 GANP M FAE Y GL+T+ ID QE+ + ++ K+FEVQ + T+H LVV + Sbjct: 182 VFGANPIPMPFAEVYTGLETRTIDAQEHPINVVWSAKFFEVQKFLSLTHHAYSPLLVVIN 241 Query: 245 SKWWDGLPADVRDQFAKILNEVTIERNAESNKVEELNKQYII----EAGGVVRTLTPEQR 300 +DGL +F + L E K+ ++Q II EAG V +T R Sbjct: 242 KAKFDGL----SPEFQQALVSSAQEAGNYQRKLVAEDQQKIIDGMKEAG--VEVITDLDR 295 Query: 301 QQWVDAL-KPVWQKFEKDI--GADLIEA 325 + + DAL V F KD+ GADL++A Sbjct: 296 KAFSDALGNQVRDMFVKDVPQGADLLKA 323 Lambda K H 0.316 0.132 0.383 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: 272 Number of extensions: 15 Number of successful extensions: 2 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: 332 Length of database: 328 Length adjustment: 28 Effective length of query: 304 Effective length of database: 300 Effective search space: 91200 Effective search space used: 91200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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