GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate AO353_17555 AO353_17555 enoyl-CoA hydratase

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



>FitnessBrowser__pseudo3_N2E3:AO353_17555
          Length = 370

 Score =  242 bits (617), Expect = 1e-68
 Identities = 141/342 (41%), Positives = 198/342 (57%), Gaps = 12/342 (3%)

Query: 16  IGHLTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCAGGDIRSLYD 75
           IG  +L+    LNA++L M+R+L  QL+AWA++PQ+  V+LRG G KAFCAGG++R+L +
Sbjct: 16  IGIASLDAEKSLNALSLPMIRALSDQLEAWAKEPQIVCVLLRGNGAKAFCAGGEVRNLVE 75

Query: 76  SFKS--GDT--LHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTE 131
           + ++  G+   L   FF  EY LD  +H Y KP++    G+VLGGG+GL+QGA +R+VT 
Sbjct: 76  ACRAHPGEVPPLAAQFFSAEYRLDFRLHTYPKPLICWGHGYVLGGGLGLLQGASIRIVTP 135

Query: 132 RSRLAMPEVAIGYFPDVGGSHFLPRVPGELGIYLGVSGVQIRAADALYCGLADWYLESNK 191
            SRLAMPE++IG +PDVG S FL R+PG+LG++LG++G Q+ A DA+   LAD +L   +
Sbjct: 136 SSRLAMPEISIGLYPDVGASWFLSRLPGKLGLFLGLTGAQMNARDAIDLDLADRFLLDEQ 195

Query: 192 LGTLDEQLDQLQWHETPLKDLQGLLAKL---AVQQLPAAPLAALRPAIDHFFALPDVPSM 248
              L E L QL W E     L  LL  L   AV ++P A     R  ID    + DV   
Sbjct: 196 QEELIEGLLQLNWQEQTPMQLNSLLKALQQEAVGKMPEAQWLPRRQQIDELLDVSDVRC- 254

Query: 249 VEQLRAVTVADSHE--WATATADLLESRSPLAMGVTLEMLRRGRHLSLEQCFALELHLDR 306
               RA+++   H        A  L    PL   +  E ++R RHLSL + F +E  +  
Sbjct: 255 --AWRAISLLRDHRDLLLARAAKNLHEGCPLTAHLVWEQIQRARHLSLAEVFQMEYTMSL 312

Query: 307 QWFERGDLIEGVRALLIDKDKNPRWSPPTLQALDAGHVASFF 348
                 +  EGVRA LIDKD+ P W  P + A+    V + F
Sbjct: 313 NCCRHPEFSEGVRARLIDKDQKPHWHWPDINAIPEAVVQAHF 354


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: 397
Number of extensions: 15
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: 370
Length adjustment: 29
Effective length of query: 327
Effective length of database: 341
Effective search space:   111507
Effective search space used:   111507
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