GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Shewanella oneidensis MR-1

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 201879 SO2741 adenosylmethionine--8-amino-7-oxononanoate aminotransferase (NCBI ptt file)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__MR1:201879
          Length = 461

 Score =  157 bits (398), Expect = 5e-43
 Identities = 115/331 (34%), Positives = 173/331 (52%), Gaps = 36/331 (10%)

Query: 12  DFDQVMV--PNYAPAAFIPVRGA----GSRVWDQSGRELIDFAGGIAVNVLGHAHPALVA 65
           DFD   +  P  +    +PV G     G  +    GR+LID        V G+ HPA++ 
Sbjct: 8   DFDSAHIWHPYTSMTRALPVFGVHSAQGCELELVDGRKLIDGTSSWWACVHGYGHPAILT 67

Query: 66  ALTEQANKLWHVS-NVFTNEPALRLAHKLVDATFAE--RVFFCNSGAEANEAAFKLARRV 122
           A+ +Q ++L HV     T+EPA+ L  KL+  T     +VF C+SG+ A E A K+A + 
Sbjct: 68  AMEQQLHQLSHVMFGGITHEPAIELCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMALQY 127

Query: 123 AHDRF-----GTEKYEIVAALNSFHGRTLFTVNV-----GGQSKYSDGF-------GPKI 165
              +        +K  I+     +HG T   ++V     G  + + +          P+ 
Sbjct: 128 WQGQDLPLAQKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVIKQCFVDAPQT 187

Query: 166 TGITHVPYNDLAALKAAVSDK---TCAVVLEPI-QGEGGVLPAELSYLQGARELCDAHNA 221
                +  +DLA ++  + ++     AV++EPI QG GG+      YL+G R LCD +N 
Sbjct: 188 PFGESLHQDDLAPMQRILREQHQDIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNV 247

Query: 222 LLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAKSLGGGF-PIAAMLTTEDLAKHLV--- 277
           LL+ DE+ TG GR+GKLFAY+H  +TPDIL   K+L GG+  +AA L T+++A+ +    
Sbjct: 248 LLILDEIATGFGRTGKLFAYEHTDITPDILCLGKALTGGYISLAATLCTDNVAQGISQSP 307

Query: 278 --VGTHGTTYGGNPLACAVAEAVIDVINTPE 306
             V  HG T+ GNPLACA A A +D+IN  E
Sbjct: 308 AGVFMHGPTFMGNPLACAAACASLDLINQQE 338


Lambda     K      H
   0.320    0.136    0.400 

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: 419
Number of extensions: 24
Number of successful extensions: 4
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: 406
Length of database: 461
Length adjustment: 32
Effective length of query: 374
Effective length of database: 429
Effective search space:   160446
Effective search space used:   160446
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