GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Escherichia coli BW25113

Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)

Query= SwissProt::Q9KWS5
         (491 letters)



>lcl|FitnessBrowser__Keio:14450 b0312 betaine aldehyde
           dehydrogenase, NAD-dependent (NCBI)
          Length = 490

 Score =  353 bits (907), Expect = e-102
 Identities = 202/492 (41%), Positives = 288/492 (58%), Gaps = 16/492 (3%)

Query: 1   MKQYRNFVDGKWVE--SSKTFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGR 58
           M + + ++ G +    S +TF+ + P +G+V+A V  A R+ VD AVK+  +  +  W  
Sbjct: 4   MAEQQLYIHGGYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQG-QKIWAS 62

Query: 59  TTAAQRVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILAT 118
            TA +R   LRR  + +  R  +    E  DTGK  S  +T+DI  G      +A ++  
Sbjct: 63  MTAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIPA 122

Query: 119 APVDSHRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPS 178
             ++  ++ L + ++   Y  R+PLGVV  I  WN P+ +  WK APALA GNA++ KPS
Sbjct: 123 --LEGSQIPLRETSFV--YTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPS 178

Query: 179 EDTPGTATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTI 238
           E TP TA  LAE+    G+P GVFN++ G G  + G+++++HP I+ ++FTG   +G  +
Sbjct: 179 EVTPLTALKLAEIYSEAGLPDGVFNVLPGVGAET-GQYLTEHPGIAKVSFTGGVASGKKV 237

Query: 239 M-RAAAEGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVE-- 295
           M  +AA  +K V+ ELGGK+  ++F D D +   D  M A F +SGQVC    RV+V   
Sbjct: 238 MANSAASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAK 297

Query: 296 -RPIFDRFCVALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAG 354
            +  F++  +A  ERI+A  V  P    T  GPL+S  HRD VL Y    ++EGA  L G
Sbjct: 298 CKAAFEQKILARVERIRAGDVFDPQ---TNFGPLVSFPHRDNVLRYIAKGKEEGARVLCG 354

Query: 355 GGVPRFGDERDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRY 414
           G V + GD  DNGAWV PTV    SDD  +VREEIFGP+  +  ++SE EVIRRANDT Y
Sbjct: 355 GDVLK-GDGFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDY 413

Query: 415 GLAATIWTTNLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFY 474
           GLAA I T +L+RAHRV   +  GI W+NTW       P GG   SGIGRE G+ +L  Y
Sbjct: 414 GLAAGIVTADLNRAHRVIHQLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVMTLQSY 473

Query: 475 SELTNVCVRIDK 486
           +++ ++ V + K
Sbjct: 474 TQVKSIQVEMAK 485


Lambda     K      H
   0.320    0.136    0.417 

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: 576
Number of extensions: 34
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: 491
Length of database: 490
Length adjustment: 34
Effective length of query: 457
Effective length of database: 456
Effective search space:   208392
Effective search space used:   208392
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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