GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Klebsiella michiganensis M5al

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BWI76_RS03070 BWI76_RS03070 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>FitnessBrowser__Koxy:BWI76_RS03070
          Length = 501

 Score =  558 bits (1439), Expect = e-163
 Identities = 274/497 (55%), Positives = 363/497 (73%), Gaps = 4/497 (0%)

Query: 6   VVGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSS 65
           + G++I G+   S + +   VF+PATG V   V L+    V  A+  A  AF +WS  + 
Sbjct: 3   ITGNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRTTP 62

Query: 66  LRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTD 125
           LRR+RVMF FK LL++H +ELA II  EHGKV SDA GE+TRG+E+VE+ACG P+L+K +
Sbjct: 63  LRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIKGE 122

Query: 126 FSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSAS 185
           FS ++G G+D+++L QPLGV AG+TPFNFP MVP+WM PLAL  GN F+LKP    P+A+
Sbjct: 123 FSSDVGTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSFVLKPPALAPTAA 182

Query: 186 LLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGK 245
           + +A LL EAGLPDGVFNVV       + L + P I A+SFVGS+ +AE+I++  +A GK
Sbjct: 183 VRLAELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRIAAVSFVGSSGVAEHIYKTASAYGK 242

Query: 246 RVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGD-VGDELIAKL 304
           RVQA G AKNH IVMPDADLD   +A++G A+GSAGERCMA+ + VAVGD   D+LIA+L
Sbjct: 243 RVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIARL 302

Query: 305 LPRIDQLKIGNGQQPG---TDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGA 361
            P ++ LK+G G   G    +MGP+V+  H+ KV G+ID GV+EGA L+VDGR  +VPG 
Sbjct: 303 KPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVPGF 362

Query: 362 EQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRD 421
           E+G++VG TLFD VT EM+I+++EIFGPVLGIVRV D+ +A+ L+N+HEFGNG + FT +
Sbjct: 363 EEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFTSN 422

Query: 422 GGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVM 481
           G  AR F   ++ GMVG+NVP+PVPMA+HSFGGWKRS+FG  + +G +G+RFY+R K+  
Sbjct: 423 GHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKTAT 482

Query: 482 QRWPDSIAKGPEFSMPT 498
            RWP       EFSMPT
Sbjct: 483 VRWPQGQQTVSEFSMPT 499


Lambda     K      H
   0.320    0.137    0.412 

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: 719
Number of extensions: 23
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: 500
Length of database: 501
Length adjustment: 34
Effective length of query: 466
Effective length of database: 467
Effective search space:   217622
Effective search space used:   217622
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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