GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Azospirillum thiophilum BV-S

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_045580995.1 AL072_RS06645 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8DQH9
         (318 letters)



>NCBI__GCF_001305595.1:WP_045580995.1
          Length = 315

 Score =  190 bits (482), Expect = 4e-53
 Identities = 117/300 (39%), Positives = 170/300 (56%), Gaps = 18/300 (6%)

Query: 12  LLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMA 71
           L++L A  +++   +     N FY+ I    G N ++ VGLNL++G++GQ SLGHAGF  
Sbjct: 12  LMVLAAAIAVLPAFLP----NNFYLDIAILAGFNAVVCVGLNLLIGYAGQISLGHAGFFG 67

Query: 72  IGAYAAAIIGSKSPTYG-AFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEI 130
           IGAYA+ ++     TYG     A+L GA + G +A  V  P LRLKG YLA+ATLG+  I
Sbjct: 68  IGAYASGVLVG---TYGWPPVLALLAGAAVVGLLAFAVAKPILRLKGHYLAMATLGIGII 124

Query: 131 IRIFIINGGSLTNGAAG-------ILGIPNF--TTWQMVYFFVVITTI-ATLNFLRSPIG 180
           + I +     LT G  G       I GI  +    W  V   +++  +  +LN + SP+G
Sbjct: 125 VSIVLRTESGLTGGPDGMMVEPFRIFGIELYGEKVWYWVVGVLLVGVVWLSLNLIDSPMG 184

Query: 181 RSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSI 240
           R+  +V   E+AAE VGV+T + K++ FV  A+ AS+AGSL A + G + P    F  SI
Sbjct: 185 RALRAVHGSEVAAEVVGVDTARFKVLVFVLSAVFASVAGSLFAHYAGLITPAKADFFKSI 244

Query: 241 NVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVMIFRPGGLLGT 300
            ++ +VVFGG+ S  GA+V A+VL +L   L      + I+    L+  M+F P GLL T
Sbjct: 245 ELVTMVVFGGMASTFGAVVGAVVLTLLPQALTMFQDYQQIVLGGILMATMVFMPKGLLPT 304


Lambda     K      H
   0.327    0.143    0.403 

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: 235
Number of extensions: 11
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: 318
Length of database: 315
Length adjustment: 27
Effective length of query: 291
Effective length of database: 288
Effective search space:    83808
Effective search space used:    83808
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 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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