GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS35145
          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:

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