Align Amino acid:proton symporter (characterized, see rationale)
to candidate CCNA_00264 CCNA_00264 C4-dicarboxylate transport protein
Query= uniprot:A0A0N9WTL5 (431 letters) >FitnessBrowser__Caulo:CCNA_00264 Length = 417 Score = 429 bits (1103), Expect = e-125 Identities = 230/415 (55%), Positives = 296/415 (71%), Gaps = 9/415 (2%) Query: 10 IAMGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLVFATLVGGIA 69 I + LGVLVGW C+ F AK A S++TDIFLR+IKMIIAPLVF TLV G+A Sbjct: 9 IIASMILGVLVGWTCNQFL-DPAGAKSAADNLSIITDIFLRLIKMIIAPLVFTTLVAGVA 67 Query: 70 SMGNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNM---DVAQHATAAVPV 126 M ++ +VGRIGA+ M WF+ AS VSL++G+ +V+L PGAGLNM DVA TA Sbjct: 68 HMEDAAAVGRIGAKTMTWFIGASAVSLVLGLLMVHLLDPGAGLNMAHVDVAMKTTAT--- 124 Query: 127 NTGDFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRITDSIEEL 186 T F+LK FI H+ P SI +AMA NEILQIVVFSLF G A+A + +I + +E+ Sbjct: 125 -TDAFTLKGFITHLVPTSIFDAMAKNEILQIVVFSLFVGTAVAALDDKA-PQILELVEQA 182 Query: 187 AKVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILILWALLFGAG 246 A++M K+T +VM AP+ +FAA+AS I TQGLG+L YGK + FY + +LWALLF AG Sbjct: 183 AQIMLKVTGFVMKLAPLAIFAALASTIATQGLGMLATYGKFVLGFYSAMGVLWALLFIAG 242 Query: 247 YLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLPLGYSFN 306 L LG+ V L +IR+P+LLAFSTASSE+AYP+ +++L K G +R+ SFVLPLGYSFN Sbjct: 243 LLVLGKRVIPLFGVIRDPVLLAFSTASSEAAYPRILDSLPKVGVRRRIVSFVLPLGYSFN 302 Query: 307 LDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVAATLPMF 366 LDGSM+Y FA +FI QA+ ++L+ QQ+ +LL LM+TSKG+AGV RAS+VV+ ATL F Sbjct: 303 LDGSMLYCTFATMFIVQAHGVELTVQQQIFMLLLLMVTSKGIAGVPRASLVVIMATLTYF 362 Query: 367 NLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSESHEEADEEEGEHAPA 421 LPEA + L++G+D LDM R+ATNVVGNS+A AVVAK E + EGE A A Sbjct: 363 GLPEAWIALVLGVDHLLDMGRSATNVVGNSVAAAVVAKWEGELDDIPPEGEAAKA 417 Lambda K H 0.325 0.138 0.392 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: 438 Number of extensions: 15 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: 431 Length of database: 417 Length adjustment: 32 Effective length of query: 399 Effective length of database: 385 Effective search space: 153615 Effective search space used: 153615 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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