GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Pseudomonas fluorescens GW456-L13

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate PfGW456L13_3316 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)

Query= reanno::pseudo6_N2E2:Pf6N2E2_612
         (526 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3316
          Length = 526

 Score =  913 bits (2359), Expect = 0.0
 Identities = 466/526 (88%), Positives = 485/526 (92%)

Query: 1   MNQILGHNYIGGARSAAGQTRLQSVDASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYR 60
           M +ILGHNYIGG RSAAG  +LQSVDA+TGEALPH F QAT +EVDAAA AAAAAYPA R
Sbjct: 1   MTRILGHNYIGGQRSAAGSIKLQSVDATTGEALPHAFYQATVQEVDAAAGAAAAAYPANR 60

Query: 61  SLSAVRRAEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRR 120
           SLSA RRA+FLEAIADELDALGD+FVAVVCRETALPA RIQGERGRTSGQMRLFAKVLRR
Sbjct: 61  SLSAERRAQFLEAIADELDALGDDFVAVVCRETALPAGRIQGERGRTSGQMRLFAKVLRR 120

Query: 121 GDFYGARIDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGC 180
           GDFYGARIDRALPER PLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGC
Sbjct: 121 GDFYGARIDRALPERQPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGC 180

Query: 181 PVVFKAHSGHMATAEHVADAIIRAAEKTLMPAGVFNMIYGGGVGEWLVKHPAIQAVGFTG 240
           PVVFKAHSGHMATAE VADAIIRAAEKT MPAGVFNMIYGGGVGE LVKHPAIQAVGFTG
Sbjct: 181 PVVFKAHSGHMATAEWVADAIIRAAEKTGMPAGVFNMIYGGGVGEALVKHPAIQAVGFTG 240

Query: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQF 300
           SLKGGRALCDMAAAR QPIPVFAEMSSINPVIVLP+AL+ RA++VARDLTASVVQGCGQF
Sbjct: 241 SLKGGRALCDMAAARAQPIPVFAEMSSINPVIVLPEALQARADTVARDLTASVVQGCGQF 300

Query: 301 CTNPGLVIGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLA 360
           CTNPGLVIGIRS  F+AF QQVA L+GDQ  QTMLNAGTL SYG+GLQKLLAHPGIEHLA
Sbjct: 301 CTNPGLVIGIRSAPFSAFVQQVAGLMGDQPAQTMLNAGTLSSYGQGLQKLLAHPGIEHLA 360

Query: 361 GRQQQGNQAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQLT 420
           G  QQGNQAQPQLFKAD SLL++GDE LQEEVFGPTTV VEVAD AQL AALNGLHGQLT
Sbjct: 361 GNPQQGNQAQPQLFKADVSLLLDGDEVLQEEVFGPTTVVVEVADHAQLMAALNGLHGQLT 420

Query: 421 ATMIGEPADFERFSELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480
           AT+IGEP DFE+F+ LT LLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG
Sbjct: 421 ATVIGEPEDFEQFAGLTALLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480

Query: 481 TLAIDRFLRPVCFQNYPDSLLPEPLKNANPLGILRLVDGVPGREAL 526
           TLAIDRFLRPVCFQNYPDSLLP+ LKN NPL I RLVDG   REAL
Sbjct: 481 TLAIDRFLRPVCFQNYPDSLLPDALKNGNPLRIQRLVDGQSSREAL 526


Lambda     K      H
   0.319    0.135    0.395 

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: 1019
Number of extensions: 22
Number of successful extensions: 1
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: 526
Length of database: 526
Length adjustment: 35
Effective length of query: 491
Effective length of database: 491
Effective search space:   241081
Effective search space used:   241081
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.

Links

Downloads

Related tools

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