GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Desulfovibrio vulgaris Hildenborough

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 209487 DVU0548 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= ecocyc::LIVH-MONOMER
         (308 letters)



>lcl|MicrobesOnline__882:209487 DVU0548 high-affinity branched-chain
           amino acid ABC transporter, permease protein
          Length = 302

 Score =  310 bits (793), Expect = 4e-89
 Identities = 156/302 (51%), Positives = 224/302 (74%), Gaps = 4/302 (1%)

Query: 7   YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66
           YF + +F G+T GS YALIA+GYTMVYGII +INFAHGEVYMIG++ + ++   L + G 
Sbjct: 5   YFCELLFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMIGAFTALIVAGVLGIYGF 64

Query: 67  DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTE 126
               +L+ A  V A++  +AYG+++E+VAY+P+R++ RL  LISAIGMSIFLQNYV L +
Sbjct: 65  PEAGILIIAAIV-AVIYCAAYGFTLEKVAYKPLRDAPRLSPLISAIGMSIFLQNYVILAQ 123

Query: 127 GSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRA 186
            S  V  P L     ++   E  +    T   +I + + + M+ LT+FI+Y+RMG+A RA
Sbjct: 124 TSDFVPFPRLVPDLAIL---EPIAHITGTSDVLIIVTSAITMVGLTLFIKYTRMGKAMRA 180

Query: 187 CAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAA 246
            A++ KMA LLGI+ DRVI+LTF+IG+++AA+ GVL+    G +N  IGF+AG+KAFTAA
Sbjct: 181 TAQNRKMAMLLGIDADRVISLTFIIGSSLAAIGGVLIASHIGQVNFAIGFIAGIKAFTAA 240

Query: 247 VLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVE 306
           VLGGIGSIPGAM GGL+LG+ E+ ++ Y+S++Y+D ++FALL+L+L+  P+GILG+P+ +
Sbjct: 241 VLGGIGSIPGAMAGGLVLGLCESFATGYVSSDYEDALAFALLVLILIFRPSGILGKPKTQ 300

Query: 307 KV 308
           KV
Sbjct: 301 KV 302


Lambda     K      H
   0.328    0.141    0.410 

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: 308
Number of extensions: 16
Number of successful extensions: 5
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: 308
Length of database: 302
Length adjustment: 27
Effective length of query: 281
Effective length of database: 275
Effective search space:    77275
Effective search space used:    77275
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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