GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Klebsiella michiganensis M5al

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate BWI76_RS24630 BWI76_RS24630 putrescine aminotransferase

Query= SwissProt::Q8ZPV2
         (408 letters)



>FitnessBrowser__Koxy:BWI76_RS24630
          Length = 468

 Score =  209 bits (532), Expect = 1e-58
 Identities = 142/385 (36%), Positives = 202/385 (52%), Gaps = 23/385 (5%)

Query: 33  LWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNEPALRLAKKLID 92
           L D QG+E+ID  GG  +  +GH +P +  A+  Q  +         +     LAK L  
Sbjct: 85  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVENQLAKQPLHSQELLDPLRAMLAKTLAA 144

Query: 93  ATFAERV--FFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRTLFTVSAGG 150
            T  +    FF NSG E+ EAALKLA+ Y   R    K   VA   AFHG++L  +SA  
Sbjct: 145 LTPGKLKYSFFSNSGTESVEAALKLAKAYQSPR---GKFTFVATSGAFHGKSLGALSATA 201

Query: 151 QPTYSQDFAPLPPDIRHAAYNDLNSASALID------DNTCAVIVEPVQGEGGVIPATKA 204
           + T+ + F PL P  RH  + D+N+   L+       D+  AVI+EP+QGEGGVI     
Sbjct: 202 KSTFRKPFMPLLPGFRHVPFGDINAMRTLLSECKKTGDDVAAVILEPIQGEGGVILPPPG 261

Query: 205 FLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTTAKALGGG-FPIGAM 263
           +L  +R+LCD   ALLI DEVQTG+GRTG+++A  H  V PDIL  AKALGGG  PIGA 
Sbjct: 262 YLPAVRKLCDEFGALLILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 321

Query: 264 LTTQDYASVM--TPGTHGTTYGGNPLATAVAGKVLDIINTPEMQNGVRQRHDAFIERLNT 321
           + T++  SV+   P  H TT+GGNPLA A A   ++++ T  +     Q+ D  ++    
Sbjct: 322 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLTQNLPAQAEQKGDMLLDGFRQ 381

Query: 322 LNVRF-GMFSEIRGLGLLLGCVLQTEFAG---KAKLIAQEAAKAGVMVLIAGGDVVRFAP 377
           L   +  + +E+RG G+L+         G    +++  Q    AG    +     +R  P
Sbjct: 382 LAREYPDLVNEVRGKGMLMAIEFVDNEIGYDFASEMFRQRVLVAGT---LNNARTIRVEP 438

Query: 378 ALNVSDEEIATGLD--RFALACERL 400
            L ++ E+    L   R ALA  R+
Sbjct: 439 PLTLTLEQCEQVLKAARLALAALRV 463


Lambda     K      H
   0.320    0.137    0.413 

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: 514
Number of extensions: 25
Number of successful extensions: 5
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: 408
Length of database: 468
Length adjustment: 32
Effective length of query: 376
Effective length of database: 436
Effective search space:   163936
Effective search space used:   163936
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 (21.8 bits)
S2: 51 (24.3 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