GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Paraburkholderia bryophila 376MFSha3.1

Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate H281DRAFT_02464 H281DRAFT_02464 betaine aldehyde dehydrogenase

Query= SwissProt::Q9KWS5
         (491 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02464 H281DRAFT_02464 betaine
           aldehyde dehydrogenase
          Length = 489

 Score =  352 bits (904), Expect = e-101
 Identities = 201/491 (40%), Positives = 278/491 (56%), Gaps = 17/491 (3%)

Query: 5   RNFVDGKWVESS--KTFQDVTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGEWGRTTAA 62
           R ++ G +V+++  +TF  V P +G  +A V +A    VD AV++     + EW   T  
Sbjct: 8   RLYIGGTYVDATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREG-QREWAALTGM 66

Query: 63  QRVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVD 122
           QR   LRR  + +  R  +    E  DTGKP++    +DI  G      +A  LATA ++
Sbjct: 67  QRSRILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAG-LATA-IE 124

Query: 123 SHRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTP 182
             ++ L   ++   Y  R+PLGV   I  WN P+ +  WK APALA GNA++ KPSE TP
Sbjct: 125 GQQIPLRPTSFV--YTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEVTP 182

Query: 183 GTATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMR-A 241
            +A  LAE+    G+PPGVFN+V G G    G  ++ HPDI  I+FTG  +TG  +M  A
Sbjct: 183 LSALKLAEIYTEAGVPPGVFNVVQGDG--RVGAMLAAHPDIEKISFTGGVETGKKVMSMA 240

Query: 242 AAEGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDR 301
            A  +K V+ ELGGK+  ++F D + E+  D  M A F +SGQVC    RV+V+R + +R
Sbjct: 241 GASSLKEVTMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVCTNGTRVFVQRSVLER 300

Query: 302 FCVALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGG---GVP 358
           F   + ER+K ++V  P +  T  GPL+S+    KVL Y +   QEGA  +AGG      
Sbjct: 301 FEALVLERVKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRLSEG 360

Query: 359 RFGDERDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAA 418
            FG     G +VEPTV  G  DD R+VREEIFGP+  +  FD+E E I RAN T YGLAA
Sbjct: 361 HFGQ----GQYVEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAA 416

Query: 419 TIWTTNLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELT 478
            + T NL+RAHRV   +  GI W+NTW       P GG   SG+GRE G+ +L  Y+ + 
Sbjct: 417 GVVTENLARAHRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIK 476

Query: 479 NVCVRIDKESP 489
           +V V +    P
Sbjct: 477 SVQVELGPYQP 487


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: 596
Number of extensions: 28
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: 491
Length of database: 489
Length adjustment: 34
Effective length of query: 457
Effective length of database: 455
Effective search space:   207935
Effective search space used:   207935
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.

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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 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, the preprint on GapMind for carbon sources, 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