GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Pseudomonas stutzeri RCH2

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate GFF1262 Psest_1295 Aspartate/tyrosine/aromatic aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__psRCH2:GFF1262
          Length = 398

 Score =  407 bits (1046), Expect = e-118
 Identities = 207/399 (51%), Positives = 277/399 (69%), Gaps = 5/399 (1%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAE-ARLNAQ 59
           +F  V+    DPIL L E F  D R +KVNL +G+YYNE+G IP L+AV EAE AR+ A 
Sbjct: 3   LFSAVEMAPRDPILGLNEAFNADTRPNKVNLGVGVYYNEEGRIPLLRAVVEAEHARIAAN 62

Query: 60  -PHGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRY 118
            P G   YLP+EG+  Y  A+  LLFG D  ++ + RV T Q LGG+GALKVGADFLKR 
Sbjct: 63  APRG---YLPIEGIAAYDAAVQKLLFGNDSSLIAEGRVVTTQALGGTGALKVGADFLKRL 119

Query: 119 FPESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLL 178
            P++ V +S+P+WENH A+F  AGF V  Y +YD + +G+    LL  LK LP RSIV+L
Sbjct: 120 LPDAVVAISNPSWENHRALFESAGFPVQNYSYYDASNHGIDRAGLLQDLKNLPPRSIVVL 179

Query: 179 HPCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLP 238
           H CCHNPTG DL  + W  ++E+L+A++ +PF+DIAYQGFG  +EEDA A+R  A +G+ 
Sbjct: 180 HACCHNPTGVDLNLEDWKQILEVLRAQDHVPFIDIAYQGFGDSIEEDAAAVRLFAESGMT 239

Query: 239 ALVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAV 298
             VS+SFSK FSLYGERVG LS++ +  E + RVL Q+K  +R NYS+PP  GA +VA+V
Sbjct: 240 FFVSSSFSKSFSLYGERVGALSMVTQSREESARVLSQVKRVIRTNYSNPPTHGATIVASV 299

Query: 299 LNDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQ 358
           LN   L+A W AE+ EMR+RI  +R  +V+ L+ +  + +F ++  QRGMFSY+GL+A Q
Sbjct: 300 LNSPELRAMWEAELGEMRSRIRELRLSMVEQLTAKGAKTDFSFVAAQRGMFSYSGLTAEQ 359

Query: 359 VDRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           V+RLR EFGVY I++GR+C A LN +N+  V  A   V+
Sbjct: 360 VERLRVEFGVYAISTGRICAAALNRSNIGHVTDAIVQVL 398


Lambda     K      H
   0.320    0.135    0.401 

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: 402
Number of extensions: 22
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: 397
Length of database: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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