GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Halomonas smyrnensis AAD6

Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_051008846.1 UYS_RS0215615 AMP-binding protein

Query= metacyc::MONOMER-20124
         (573 letters)



>NCBI__GCF_000265245.1:WP_051008846.1
          Length = 574

 Score =  172 bits (435), Expect = 4e-47
 Identities = 162/540 (30%), Positives = 234/540 (43%), Gaps = 50/540 (9%)

Query: 56  RDNTSLVYGSVRYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIYELHFAVPM 115
           RD     +  +RY W +      + A AL   LG++ GD V  +S N  E     FA   
Sbjct: 49  RDALISRHQGLRYRWRELQTEVDRAARALMA-LGVAKGDRVGIWSPNTAEWAITQFATAK 107

Query: 116 AGGILCTLNARNDSAMVSTLLAHSEAKLIFVEPQLLETARAA--------LDLLAQKDIK 167
            G IL  +N    +  +   L  S    + ++ Q   T   A        LD +   D+K
Sbjct: 108 IGAILVNINPSYRTHELEYALRQSGTSTLILQGQFKTTDYVAMLAELVPELDDVTPADLK 167

Query: 168 PPTL-----VLLTDSESFTSSSYDHYNHLL-ANGSDDFEI--RRPKNEWD-PISINYTSG 218
              L     V+  D     S  +     L  A+   D ++  R+   E+D PI+I YTSG
Sbjct: 168 SGALPDLRRVICLDGARALSGMHSWETMLTHADRVSDAQLAERQAGLEFDEPINIQYTSG 227

Query: 219 TTARPKAVVYSHRGAYLNSIATVLLHGMGTTSVYLWSVPMFHCNGWCFP-WGAAAQGATN 277
           TT  PK    SH     N         +      +  VP++HC G      G    GA  
Sbjct: 228 TTGAPKGATLSHHNILNNGFFVARTLDLSEADRMVIPVPLYHCFGMVMGNLGCMTHGAAM 287

Query: 278 ICIRK-VSPKAIFDNIHLHKVTHFGAAPTVLNMIVNSPEGNLHTPLPHKVEVMTGGSPPP 336
           I       P+A    +   + T     PT+    +  PE         +  VM G   P 
Sbjct: 288 IYPGDGFDPQATLAAVAEERATALYGVPTMFIAELEHPEFEHFDLSSLRTGVMAGSICPI 347

Query: 337 P---KVIARMEEMGFQVNHIYGLTETCGPAANCVCKPEWDALQPEERYALKARQGLNHLA 393
               KVI RM   G  +   YG+TET  P +    +   DA  P E+          HL 
Sbjct: 348 EVMRKVIERMHMQGVTI--CYGMTET-SPVS---LQTRTDA--PLEKRVTTVGSIHPHL- 398

Query: 394 MEEMDVRDPVTMESVRADGATI-----GEVMFRGNTVMSGYFKDLKATEEAFE-GGWFRS 447
             E+ + DP T       GA +     GE+  RG +VM GY+ + +AT +A +  GW  +
Sbjct: 399 --EVKLVDPGT-------GAVVPRGEPGELCTRGYSVMLGYWHNEEATAKAIDDAGWMHT 449

Query: 448 GDLGVKHEDGYIQLKDRKKDVVISGGENISTVEVETVLYSHEAVLEAAVVARPDKLWGET 507
           GDL    +DGY+ +  R KD++I GGENI   E+E  LY+H A+ +  V+  PD  +GE 
Sbjct: 450 GDLATMDDDGYVAIVGRIKDMIIRGGENIYPREIEDFLYTHPAISDVQVIGVPDDKYGEE 509

Query: 508 PCAFVTLKEGFDNDVSADQIIKFCRDRLPHYMAPKTVVF-EELPKTSTGKIQKYILKEKA 566
             A+V L E  D  +  D +  FC+ R+ HY  P+ V F ++ P T TGKIQK+ ++E+A
Sbjct: 510 VMAWVKLAE--DETLDEDGLKAFCQGRIAHYKIPRYVKFVDDFPMTVTGKIQKFKMREEA 567


Lambda     K      H
   0.318    0.133    0.408 

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: 730
Number of extensions: 44
Number of successful extensions: 6
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: 573
Length of database: 574
Length adjustment: 36
Effective length of query: 537
Effective length of database: 538
Effective search space:   288906
Effective search space used:   288906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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.

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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