Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 6936665 Sama_0852 hypothetical protein (RefSeq)
Query= reanno::ANA3:7023996 (213 letters) >FitnessBrowser__SB2B:6936665 Length = 207 Score = 162 bits (411), Expect = 3e-45 Identities = 86/204 (42%), Positives = 130/204 (63%), Gaps = 11/204 (5%) Query: 12 LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLA 71 L G A+TGALAAGR +MD FGV ++ TA+GGGT+RD ++G P+ W+ + +YL+ Sbjct: 9 LCGTAVFALTGALAAGRHRMDPFGVTVLAAVTAVGGGTIRDAIIGATPVFWLRDPNYLIV 68 Query: 72 IAFASLLTVAIAPVMRYLSKLFLAI-DALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTG 130 I T+ R + + L I DALGLA+F+++GAQK L LG + AV+MGL+TG Sbjct: 69 ILATVGFTLVFIRRPRKVPQYTLPIADALGLALFTVIGAQKALSLGLNGMSAVIMGLITG 128 Query: 131 VFGGVIRDILCNQVPLIFKKELYAVISL-----FTAGLYITLNAYQLAEWINLVVCLTLG 185 V GG+IRD+LC Q+P++ + E+YA S+ +T L + +N+ Q A W++++ L Sbjct: 129 VGGGIIRDVLCRQIPMVLRTEIYATASILGGIAYTLSLQLGMNS-QTALWLSMLSALI-- 185 Query: 186 FSLRMLALRYHWSMPTFDYQANGD 209 LR+ A+R+H S+P FD + D Sbjct: 186 --LRLAAIRWHLSLPAFDLKTRRD 207 Score = 38.1 bits (87), Expect = 1e-07 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 1/71 (1%) Query: 93 FLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVPLIFKKE- 151 F D G AVF++ GA P V+ VT V GG IRD + P+ + ++ Sbjct: 4 FYFFDLCGTAVFALTGALAAGRHRMDPFGVTVLAAVTAVGGGTIRDAIIGATPVFWLRDP 63 Query: 152 LYAVISLFTAG 162 Y ++ L T G Sbjct: 64 NYLIVILATVG 74 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: 152 Number of extensions: 7 Number of successful extensions: 5 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