GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Pseudomonas stutzeri RCH2

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate GFF3052 Psest_3110 Enoyl-CoA hydratase/carnithine racemase

Query= reanno::pseudo1_N1B4:Pf1N1B4_4790
         (356 letters)



>FitnessBrowser__psRCH2:GFF3052
          Length = 367

 Score =  223 bits (567), Expect = 8e-63
 Identities = 140/345 (40%), Positives = 184/345 (53%), Gaps = 12/345 (3%)

Query: 20  TLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCAGGDIRSLYDSFKS 79
           TL+    LNA++L M+ +L  +   WA DP V  V+LRG G KAFCAGGD+R L ++ ++
Sbjct: 20  TLDAAQQLNALSLPMIEALLDRFARWAADPDVVCVLLRGNGIKAFCAGGDVRRLAEACRA 79

Query: 80  GD----TLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTERSRL 135
                  L E FF +EY L   +HHY KP+L    G+V+GGGMGL+QGA +R+VT  SRL
Sbjct: 80  APGVVPALAERFFADEYRLVHLMHHYPKPLLCWGHGYVMGGGMGLLQGAAIRIVTPDSRL 139

Query: 136 AMPEVAIGYFPDVGGSHFLPRVPGELGIYLGVSGVQIRAADALYCGLADWYLESNKLGTL 195
           AMPEVAIG   DVG S FLPR+PG+LG++ G++G +  A DAL  GLAD  L   +   L
Sbjct: 140 AMPEVAIGLHTDVGASWFLPRLPGKLGLFAGLTGFRFNARDALDVGLADRCLTKEQQPDL 199

Query: 196 DEQLDQLQWHETPLKDLQGL---LAKLAVQQLPAAPLAALRPAIDHFFALPDVPSMVEQL 252
            E L Q+ W E     L  L   L K A  +LP   L   R  ID    + ++    + L
Sbjct: 200 IEGLVQINWQEYAAGQLHSLLRALGKQASDKLPEGRLLKRRDRIDELLDVAELAHAWQAL 259

Query: 253 RAVTVADSHEWATATADLLESRSPLAMGVTLEMLRRGRHLSLEQCFALELHLDRQWFERG 312
            A+  +D  +     A  L    PL+  +      RGR  SL Q   +E  L        
Sbjct: 260 AALH-SDPDDVFAEAAHALGKACPLSAHLIWNQQARGRKQSLTQALQMEYALSLNCCRHP 318

Query: 313 DLIEGVRALLIDKDKNPRWSPPTL----QALDAGHVASFFTGFDP 353
           +  EGVRA LIDKD  P W  P      QA+ A H  + + G  P
Sbjct: 319 EFAEGVRARLIDKDNQPNWHWPDALNIPQAVIAAHFQAPWAGAHP 363


Lambda     K      H
   0.322    0.138    0.422 

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: 390
Number of extensions: 14
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: 356
Length of database: 367
Length adjustment: 29
Effective length of query: 327
Effective length of database: 338
Effective search space:   110526
Effective search space used:   110526
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 (21.9 bits)
S2: 49 (23.5 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