GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate AO353_04605 AO353_04605 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_16280
         (223 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04605
          Length = 365

 Score =  139 bits (350), Expect = 7e-38
 Identities = 74/220 (33%), Positives = 123/220 (55%), Gaps = 7/220 (3%)

Query: 4   DFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFR 63
           D  G+       W G+++TL +  +G+VG + LG +LAL R S+   +  +   ++ ++R
Sbjct: 143 DILGLTNVATSQWGGLMLTLVIATVGIVGALPLGIMLALGRRSNLPAIRVVCVTFIEFWR 202

Query: 64  SIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPK 123
            +PL+ V+    + +P  L     E          ++  ++F++AY  E+VR G+Q+IPK
Sbjct: 203 GVPLITVLFMSSVMLPLFLP----EGMNFDKLLRALIGVILFQSAYVAEVVRGGLQAIPK 258

Query: 124 GQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATR 183
           GQ  AA A+G+GY + M L+ILPQA + + P ++   I LF+DTSLV  +GL D LN+ +
Sbjct: 259 GQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVK 318

Query: 184 ---ASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQKR 220
              A    +G A E  + A LV++   F  SR    L+++
Sbjct: 319 QAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERK 358


Lambda     K      H
   0.331    0.143    0.425 

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: 226
Number of extensions: 9
Number of successful extensions: 1
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: 223
Length of database: 365
Length adjustment: 26
Effective length of query: 197
Effective length of database: 339
Effective search space:    66783
Effective search space used:    66783
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 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:

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