GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas baetica a390

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_100845694.1 C0J26_RS16980 AMP-binding protein

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_003031005.1:WP_100845694.1
          Length = 565

 Score =  168 bits (425), Expect = 6e-46
 Identities = 148/543 (27%), Positives = 244/543 (44%), Gaps = 51/543 (9%)

Query: 27  FLERAGKYFKDKTAVV-YRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEF 85
           F +   +Y   +  VV ++  RY++    D V + A AL+  G    D+L   + N  ++
Sbjct: 30  FAQTVAQYPDGEALVVRHQQLRYSWRQLADAVDLNARALLALGLQTGDRLGIWAPNCAQW 89

Query: 86  LESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNS---------LLEV 136
             + F     G +LV IN      E+ Y++  +  +++V    + +S         + E+
Sbjct: 90  CITQFATAKIGVILVNINPAYRSSELEYVLKQAGCQWLVCAGAFKSSNYHGMLQGLVPEL 149

Query: 137 KDQIKAEI----------ILLEDPDNPSA----SETARKEVRMTYRELVKGGSRDPLPIP 182
            +Q   E+          ++  D   PS     S+ A   V ++  +L +         P
Sbjct: 150 AEQSIGELRSERLPDLRGVISLDAQPPSGFLPWSQLADLAVTVSPEQLRERSDSLHFDQP 209

Query: 183 AKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAAS 242
                  + + YTSGTTG PKG    H     N         +      +  +P++H   
Sbjct: 210 -------VNIQYTSGTTGFPKGATLSHYNILNNGYMVGESIGLTPLDRLVIPVPLYHCFG 262

Query: 243 WGF-SWATVAVGATNVC-LDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKF 300
               +   +  G+T +   D  D  L  + V +E+ T +   PT+++ + D  +R     
Sbjct: 263 MVMGNLGCITHGSTMIYPNDAFDPLLTLQTVAEEKATGLYGVPTMFIAMLDQPQRTEFDL 322

Query: 301 SNRVHMLVAGA-APAPATLKAMQEIGGYMCHV---YGLTETYGPHSICEWRREWDSLPLE 356
           S+    ++AGA  P     + + E+  +M  V   YG+TET  P S+        + P +
Sbjct: 323 SSLRTGIMAGATCPIEVMRRVISEM--HMSEVQIAYGMTET-SPVSL-------QTGPND 372

Query: 357 EQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESF 416
           E        G      E  + D  G  VP     IGE+  RG++V LGY+ NP+ TAE+ 
Sbjct: 373 ELELRVTTVGRTQPQLESKIIDEAGNLVP--RGIIGELCTRGYSVMLGYWNNPQATAEAI 430

Query: 417 RD-GWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGT 475
            + GW H+GD A ++ DGY+ I  R KD+I  GGE +    +E+     P V  V V G 
Sbjct: 431 DEAGWMHTGDLASMNDDGYVNIAGRNKDMIIRGGENIYPRELEEFFFTHPAVADVQVVGI 490

Query: 476 PDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKY 534
           P  ++GE + A I+   G   +E E+  +CKER+AHF+ P+  +F    PMT TGK+QK+
Sbjct: 491 PCSRYGEEIVAWIKFHPGHSASELELQTWCKERIAHFKTPRHFKFVDEFPMTVTGKIQKF 550

Query: 535 VLR 537
            +R
Sbjct: 551 RMR 553


Lambda     K      H
   0.319    0.136    0.411 

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: 660
Number of extensions: 29
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 549
Length of database: 565
Length adjustment: 36
Effective length of query: 513
Effective length of database: 529
Effective search space:   271377
Effective search space used:   271377
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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