Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 14303 b0157 conserved inner membrane protein (NCBI)
Query= reanno::ANA3:7023996 (213 letters) >FitnessBrowser__Keio:14303 Length = 207 Score = 139 bits (351), Expect = 3e-38 Identities = 78/203 (38%), Positives = 120/203 (59%), Gaps = 10/203 (4%) Query: 12 LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLA 71 ++G A++G L AG+ +MD FGV+++G TA+GGGT+RDM L + P+ WV++ L+ Sbjct: 8 IVGTAVFAISGVLLAGKLRMDPFGVLVLGVVTAVGGGTIRDMALDHGPVFWVKDPTDLVV 67 Query: 72 IAFASLLTVAIAPVMRYLSKLFL-AIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTG 130 S+LT+ + R L K L +DA+GLAVF +G K P IAV MG++TG Sbjct: 68 AMVTSMLTIVLVRQPRRLPKWMLPVLDAVGLAVFVGIGVNKAFNAEAGPLIAVCMGVITG 127 Query: 131 VFGGVIRDILCNQVPLIFKKELYA----VISLFTAGLYITLNA-YQLAEWINLVVCLTLG 185 V GG+IRD+L ++P+I + E+YA + + A Y T + + A + +VV L Sbjct: 128 VGGGIIRDVLAREIPMILRTEIYATACIIGGIVHATAYYTFSVPLETASMMGMVVTLL-- 185 Query: 186 FSLRMLALRYHWSMPTFDYQANG 208 +R+ A+R+H +PTF NG Sbjct: 186 --IRLAAIRWHLKLPTFALDENG 206 Score = 42.4 bits (98), Expect = 6e-09 Identities = 28/84 (33%), Positives = 46/84 (54%), Gaps = 3/84 (3%) Query: 96 IDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVPLIFKKE-LYA 154 +D +G AVF+I G L P +V+G+VT V GG IRD+ + P+ + K+ Sbjct: 6 LDIVGTAVFAISGVLLAGKLRMDPFGVLVLGVVTAVGGGTIRDMALDHGPVFWVKDPTDL 65 Query: 155 VISLFTAGLYITL--NAYQLAEWI 176 V+++ T+ L I L +L +W+ Sbjct: 66 VVAMVTSMLTIVLVRQPRRLPKWM 89 Lambda K H 0.330 0.143 0.438 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: 151 Number of extensions: 11 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 213 Length of database: 207 Length adjustment: 21 Effective length of query: 192 Effective length of database: 186 Effective search space: 35712 Effective search space used: 35712 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: 45 (21.9 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