Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= uniprot:A3DE71 (289 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 148 bits (373), Expect = 2e-40 Identities = 84/268 (31%), Positives = 154/268 (57%), Gaps = 11/268 (4%) Query: 25 LAILVVLTLGPIVFMVLTSLMDHN-AIARGKWIAPTR--FSNYVEVFQKLPFGIYFRNSL 81 L +L +++L P+++MV S+M A + P+ F+NY E+F + G+ F NSL Sbjct: 19 LLVLALVSLAPLLWMVSVSVMPAGEATTFPPPLTPSHVTFANYHELFARTGMGVNFANSL 78 Query: 82 IVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVKIKQ 141 +V + + +L++ T+AGY+ AK +F G +++A ++P + +LPL+L +KQ Sbjct: 79 LVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFL---LMKQ 135 Query: 142 ATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLRVML 201 + L+NS G+++ A F I+++R + SIP EL EAAR+DG + F +++L Sbjct: 136 ---LGLVNSFGGVIV--PALATVFGIFLVRQYARSIPDELLEAARMDGAGEMRIFFQIVL 190 Query: 202 PLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTARYDLLMAAGT 261 P+ P +V +I+ F+ AW++ ++ ++L D + T+P + +++MA Sbjct: 191 PMLKPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATLSREHIMDVEMMMAGAV 250 Query: 262 IVTIPVLIMFFTMQKKFISGMTAGAVKG 289 + IPVL +F +Q+ +I G+ G+VKG Sbjct: 251 VTVIPVLALFLLLQRYYIQGLMLGSVKG 278 Lambda K H 0.332 0.145 0.434 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: 221 Number of extensions: 12 Number of successful extensions: 3 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: 289 Length of database: 278 Length adjustment: 26 Effective length of query: 263 Effective length of database: 252 Effective search space: 66276 Effective search space used: 66276 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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