GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_02464
          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 (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