GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluD in Pseudomonas stutzeri RCH2

Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::P48245
         (273 letters)



>lcl|FitnessBrowser__psRCH2:GFF136 Psest_0136 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          Length = 229

 Score =  100 bits (250), Expect = 2e-26
 Identities = 74/225 (32%), Positives = 113/225 (50%), Gaps = 13/225 (5%)

Query: 13  WTPFINSQTWTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIET 72
           W  FI    W    + G W TL+    SVI  L++   LG+ R S    +R      I  
Sbjct: 3   WEIFIK---WLPSFIDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFF 59

Query: 73  FRAIPVLILMIFAYQMFAQYNIVPSSQL------AFAAVVFGLTMYNGSVIAEILRSGIA 126
           FR  P+L+ +   Y   AQ+++V  S L       +   +  +T++  + IAEI+R  I 
Sbjct: 60  FRGTPLLVQLFLVYYGMAQFDVVRQSALWPYLRDPYWCAIITMTLHTAAYIAEIIRGAIQ 119

Query: 127 SLPKGQKEAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVV 186
           ++P G+ EAA ALGMS  Q    I+LP+A    LPA  +++++ LK SAL   I  +E+ 
Sbjct: 120 NVPHGEIEAARALGMSRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLEL- 178

Query: 187 RSGIQSASVNRNYL-AALFVVA-LIMIVLNFSLTALASRIERQLR 229
            +G+      R YL   +F+ A LI +++ F L      +ER LR
Sbjct: 179 -TGMARKIAARTYLHEEMFLTAGLIYLLIAFILMQGFKLLERWLR 222


Lambda     K      H
   0.323    0.136    0.395 

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: 142
Number of extensions: 8
Number of successful extensions: 2
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: 273
Length of database: 229
Length adjustment: 24
Effective length of query: 249
Effective length of database: 205
Effective search space:    51045
Effective search space used:    51045
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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