GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Cupriavidus basilensis 4G11

Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate RR42_RS04830 RR42_RS04830 2,5-dioxovalerate dehydrogenase

Query= SwissProt::Q08IC0
         (525 letters)



>FitnessBrowser__Cup4G11:RR42_RS04830
          Length = 525

 Score =  644 bits (1662), Expect = 0.0
 Identities = 341/523 (65%), Positives = 397/523 (75%), Gaps = 2/523 (0%)

Query: 1   MQLTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYR 60
           M +TGEMLIGA AV G+   L A +P+ GE + AP F     A+ ERAC LA  AFD YR
Sbjct: 1   MTITGEMLIGASAVRGTTKILHATNPATGEVL-APEFHGGGAAEAERACALAEAAFDTYR 59

Query: 61  AQPLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRD 120
                 RA FLE+IA  + ALGD LIERAHAE+ LPVARLQGER RT GQLRLFA V+RD
Sbjct: 60  NTSPETRARFLESIASGLEALGDTLIERAHAESALPVARLQGERARTAGQLRLFASVLRD 119

Query: 121 GRFLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGC 180
           GR+ +A++D A P RTP PR DLRLQK+ +GPV VFGASNFPLAFSVAGGDTASALAAGC
Sbjct: 120 GRWQSATLDSALPERTP-PRPDLRLQKIAVGPVAVFGASNFPLAFSVAGGDTASALAAGC 178

Query: 181 PVIVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGF 240
           PV+VKAH AHLGTSELVGR I+ AVA  G+P GVFSLLVG G  +G ALV+HP++QAVGF
Sbjct: 179 PVVVKAHSAHLGTSELVGRVIQKAVADAGLPEGVFSLLVGAGVAVGTALVAHPSIQAVGF 238

Query: 241 TGSRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVG 300
           TGSR GG+ALVQ AN+RPQPIPVYAEMSSINPV L PAALAARG  IA   VDSL +GVG
Sbjct: 239 TGSRSGGLALVQTANSRPQPIPVYAEMSSINPVFLLPAALAARGAQIARNLVDSLVMGVG 298

Query: 301 QFCTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVRE 360
           QFCTNPGL+LA++ P LD F   A  ALA+K A  MLT GI+ AY NG  +L+++ G+R 
Sbjct: 299 QFCTNPGLLLAVESPALDVFRQGAIAALAEKAAATMLTPGISQAYDNGVAQLSDIEGLRR 358

Query: 361 IGAGEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEG 420
           IG+G+ A    QA  AL+E  A+ FLA+     EVFGP+S++V CRD +E+  V   LEG
Sbjct: 359 IGSGQTASGPNQARPALFETTAERFLADHRMEAEVFGPSSVLVVCRDHEEMLAVARRLEG 418

Query: 421 QLTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVT 480
           QLTAT+Q DA D+  A  LL VLERKAGR+L NGYPTGVEV  AMVHGGPFPATS+   T
Sbjct: 419 QLTATVQADAGDRAEAGSLLTVLERKAGRVLFNGYPTGVEVSYAMVHGGPFPATSDTRAT 478

Query: 481 SVGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPRLRDGK 523
           SVGA+AIERFLRPVCYQ+ P +LLP  LQ+ NPL + RL DG+
Sbjct: 479 SVGASAIERFLRPVCYQNVPAELLPPALQDGNPLKVWRLTDGQ 521


Lambda     K      H
   0.320    0.137    0.396 

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: 908
Number of extensions: 42
Number of successful extensions: 3
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: 525
Length of database: 525
Length adjustment: 35
Effective length of query: 490
Effective length of database: 490
Effective search space:   240100
Effective search space used:   240100
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