GapMind for catabolism of small carbon sources

 

Aligments for a candidate for boxD in Cupriavidus basilensis 4G11

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate RR42_RS35145 RR42_RS35145 aldehyde dehydrogenase

Query= BRENDA::Q13WK4
         (531 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS35145 RR42_RS35145 aldehyde
           dehydrogenase
          Length = 514

 Score =  663 bits (1710), Expect = 0.0
 Identities = 341/522 (65%), Positives = 397/522 (76%), Gaps = 8/522 (1%)

Query: 1   MTELLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRAL 60
           MTELL N++ G+W AG+GAG TL+DPV G ALVRV + GLDLA  F+FARE GGAALRA+
Sbjct: 1   MTELLSNYLGGRWQAGSGAGATLSDPVLGDALVRVDATGLDLAAGFAFAREQGGAALRAM 60

Query: 61  TYAQRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120
           TY +RAA LA IVK+LQ  R  YY IATANSGT  NDSAVDIDGGIFTL  YAKLG +LG
Sbjct: 61  TYRERAAMLAAIVKILQTNRDAYYEIATANSGTVHNDSAVDIDGGIFTLGTYAKLGDALG 120

Query: 121 EVHALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180
           E   L DG A  L KD  F +QHVL PTRGVAL INAFNFPSWGLWEKAAPALL+GVPVI
Sbjct: 121 ERRYLIDGDAARLGKDPLFQSQHVLVPTRGVALLINAFNFPSWGLWEKAAPALLAGVPVI 180

Query: 181 VKPATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAAT 240
           VKPATATAWLTQRMV DVVDAG+LPPGALS++CGS+AGLLDQ++ FDVVSFTGSA TAA 
Sbjct: 181 VKPATATAWLTQRMVRDVVDAGVLPPGALSVVCGSAAGLLDQLQPFDVVSFTGSAQTAAL 240

Query: 241 LRAHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300
           +R+H A  QR  R+N+EADS+NSA+L       + AFDL  KE  REMTVKSGQKCTAIR
Sbjct: 241 IRSHAAVTQRSVRVNIEADSVNSALLLPGEAAGSEAFDLLAKEAAREMTVKSGQKCTAIR 300

Query: 301 RAFVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVL 360
           R FVPEA      +A+ A+LA++TVGNPR++AVRMG+LVSR Q  +V  G+  L+ +A +
Sbjct: 301 RIFVPEALYGAAADAIGARLARVTVGNPRHEAVRMGALVSRAQLASVREGLGYLQAQAEV 360

Query: 361 AYDSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420
            +D +   L+DAD  +A CV P L    D   A  +HD EVFGPVA++ PYR   D    
Sbjct: 361 LHDGATHALVDADPAVACCVGPTLLGARDAHAADRVHDTEVFGPVATLVPYRDNAD---- 416

Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480
               A+AL RRGQGSLVAS+Y +D   L + A+ELADSHGRVH ISP V    TGHGNVM
Sbjct: 417 ----ALALVRRGQGSLVASLYGSDADALAKAAVELADSHGRVHVISPDVAQLHTGHGNVM 472

Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTL 522
           P SLHGGPGRAGGGEELGGLRAL FYHRRSA+QA+++ +  L
Sbjct: 473 PQSLHGGPGRAGGGEELGGLRALNFYHRRSAVQASTSVLAQL 514


Lambda     K      H
   0.318    0.132    0.379 

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: 739
Number of extensions: 28
Number of successful extensions: 2
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: 531
Length of database: 514
Length adjustment: 35
Effective length of query: 496
Effective length of database: 479
Effective search space:   237584
Effective search space used:   237584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 (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 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