GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Dechlorosoma suillum PS

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Dsui_1464 Dsui_1464 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::Q72IB9
         (516 letters)



>lcl|FitnessBrowser__PS:Dsui_1464 Dsui_1464 NAD-dependent aldehyde
           dehydrogenase
          Length = 506

 Score =  210 bits (535), Expect = 9e-59
 Identities = 165/487 (33%), Positives = 236/487 (48%), Gaps = 38/487 (7%)

Query: 31  REEFGRHYPLYIGGEWV-DTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKT 89
           + ++   Y  +IGG+WV   K +   +      +     A++G  + E AL+AA  A   
Sbjct: 12  KHQYKARYDNFIGGKWVAPVKGQYFDVITPITGKPYTQAAQSGAEDIELALDAAHAAADK 71

Query: 90  WKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEA-SADVAEAIDFIEYYARA 148
           W      +RS +LLK A  +      L      + GK   E  +AD+  A D   Y+A  
Sbjct: 72  WGKTSATERSNILLKIADRIEANLEMLAYVETVDNGKAIRETLNADIPLAADHFRYFA-G 130

Query: 149 ALRYRYPAVEVVPYPGEDNE---SFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVI 205
            LR +  ++  +    ++N     F+ PLG    I PWNFP+ +    +   +  GN V+
Sbjct: 131 CLRSQEGSISEI----DENTIAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVV 186

Query: 206 AKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVG 265
            KPAE   +    + E+  +   PPGV+N + G G + G  L    R   I FTGS   G
Sbjct: 187 LKPAESTPISILVLAELIADL-LPPGVLNIVNGYGRDAGMALASSKRIAKIAFTGSTATG 245

Query: 266 LKIYEAAGR-LAPGQTWFKRAYVETGGK-------DAIIVDETADFDLAAEGVVVSAYGF 317
             I +AA   L P       A +E GGK       D    D+   FD A EG+V+ A+  
Sbjct: 246 RVIAQAAANSLIP-------ATLELGGKSPNIFFADVAAADDDF-FDKAIEGLVLFAFN- 296

Query: 318 QGQKCSAASRLILTQGAYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYI 376
           QG+ C+  SR ++ +  Y+  +ERVL R + +  G P + +  +G   S  Q  K++SY+
Sbjct: 297 QGEVCTCPSRALIHESIYDHFMERVLARVKAIKQGSPLDTDSMMGAQASQMQMDKIMSYL 356

Query: 377 EIGKNEG-QLVLGGKRLE-----GEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKD 430
            IGK EG Q ++GG R        EGY+I PT+F +   K RI QEEIFGPVL+V   K 
Sbjct: 357 AIGKEEGAQCLVGGDRARLGGELAEGYYIQPTLF-KGHNKMRIFQEEIFGPVLAVTTFKT 415

Query: 431 FAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKL 490
            AEALE+ANDTPYGL  GV+SR         R    G ++ N     A      FGG+K 
Sbjct: 416 EAEALEIANDTPYGLGAGVWSRDGNTAYRMGRGIKAGRVWTN--CYHAYPAHATFGGYKE 473

Query: 491 SGTNAKT 497
           SG   +T
Sbjct: 474 SGIGRET 480


Lambda     K      H
   0.319    0.137    0.403 

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: 566
Number of extensions: 31
Number of successful extensions: 7
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: 516
Length of database: 506
Length adjustment: 35
Effective length of query: 481
Effective length of database: 471
Effective search space:   226551
Effective search space used:   226551
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 (21.7 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, 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