GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kbl in Shewanella amazonensis SB2B

Align 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial; AKB ligase; Aminoacetone synthase; Glycine acetyltransferase; EC 2.3.1.29 (characterized)
to candidate 6937269 Sama_1439 8-amino-7-oxononanoate synthase (RefSeq)

Query= SwissProt::Q0P5L8
         (419 letters)



>FitnessBrowser__SB2B:6937269
          Length = 385

 Score =  157 bits (397), Expect = 5e-43
 Identities = 114/386 (29%), Positives = 176/386 (45%), Gaps = 22/386 (5%)

Query: 31  LEEELESIRGAGTWKSERVITSRQGPHIHVDGAPGGIINFCANNYLGLSSHPEVIQAGLR 90
           L E       AG W+  +    R  P          +++F AN+YLGL+    + +A   
Sbjct: 8   LAEARVKAESAGLWRQRQ----RHSP---------ALMDFSANDYLGLARDERLAEALAE 54

Query: 91  TLKEFGAGLSSVRFICGTQSIHKDLEAKIARFHQREDAILYPSCFDANTGLFEALLTSED 150
             + +G G  +   + G    H +LEA +      E A+L+ S F AN  L  AL  S D
Sbjct: 55  GARRYGVGSGASPLVSGYSEAHAELEAALCAATGHEAALLFCSGFAANLALCHALFDSTD 114

Query: 151 AVLSDELNHASIIDGIRLCKAHKYRYRHLDMADLEAKLQEAQKHRLRLVATDGAFSMDGD 210
            +++D+L HAS+IDGI    A+  RY H D++     ++      L    T+  FSMDGD
Sbjct: 115 TLVADKLIHASMIDGILGSGANLKRYPHCDLSGAARLIERFPGTAL---LTESIFSMDGD 171

Query: 211 IAPLQEICRLASQYGALVFVDESHATGFLGATGRGTDELLGVMDQVTIINSTLGKALGGA 270
           +APL  +  L   + +L  VD++H  G +G    G   L GV   + ++  T GKAL G 
Sbjct: 172 LAPLLPLSNLCESHNSLFIVDDAHGFGVIGEQAMGASRLDGVNISLQLV--TFGKAL-GC 228

Query: 271 SGGYTTGPGALVSLLRQRARPYLFSNSLPPAAVGCASKALDLLMESNAIVQSMAAKTLRF 330
            G    G  AL+  L   AR Y++S +L PA    A  +L L+ +      ++A     F
Sbjct: 229 QGAAVLGSQALIESLVASARHYIYSTALSPAQAHAARVSLSLVQQGEKSA-TLAVNIRHF 287

Query: 331 RSQMEAAGFTISGANHPICPVMLGDARLALNIADDMLKRGIFVIGFSYPVVPKGKARIRV 390
            +  +  G  +  +  PI  + +   +  L  AD +  RG  V     P VP    R+R+
Sbjct: 288 LNCAKEVGLALLPSQSPIQLMPVPTVQACLMAADTLKARGFLVGAIRPPTVP--APRLRI 345

Query: 391 QISAVHSEEDIDRCVEAFVEVGRLHG 416
            +SA  S   I+  V A  ++ +  G
Sbjct: 346 TLSAAQSMNSIEALVNALADIEKGFG 371


Lambda     K      H
   0.321    0.136    0.397 

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: 367
Number of extensions: 19
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: 419
Length of database: 385
Length adjustment: 31
Effective length of query: 388
Effective length of database: 354
Effective search space:   137352
Effective search space used:   137352
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: 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