GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Pseudomonas fluorescens FW300-N2E2

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf6N2E2_859 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)

Query= reanno::WCS417:GFF2159
         (526 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_859 Ketoglutarate
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 526

 Score =  826 bits (2133), Expect = 0.0
 Identities = 409/526 (77%), Positives = 462/526 (87%)

Query: 1   MTSFLGHNYIGGQRSANGSVTLQSVDATSGEALPQHFYQATPQEVDAAAKAAAQAYPAYR 60
           M+   G N+IGGQRSA G++ ++SVDA++GE LP  F+QAT QEV+ AA AA  A+ +YR
Sbjct: 1   MSLITGQNFIGGQRSAAGTIIVKSVDASTGETLPYAFHQATAQEVENAAHAAHHAFSSYR 60

Query: 61  ALSAARRAQFLDAVADELDALGDEFVELVCRETALPAARIKGERGRTSGQMRLFATVLRR 120
            LSA++RA+FLDA+A EL+AL DEF+ LVCRETALP ARI+GER RTSGQMRLFA VLRR
Sbjct: 61  TLSASKRAEFLDAIAQELEALDDEFIALVCRETALPVARIQGERARTSGQMRLFANVLRR 120

Query: 121 GDFYGARIDKALPDRQPMPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC 180
           GDFYGARID+ALP R+P+PRPDLRQYR  +GPVAVFGASNFPLAFSTAGGDTA+ALAAGC
Sbjct: 121 GDFYGARIDQALPLRKPLPRPDLRQYRTAIGPVAVFGASNFPLAFSTAGGDTASALAAGC 180

Query: 181 PVVFKAHSGHMATAERVADAIIRAAEATEMPAGVFNMIFGGGVGEALVKHPAIQAVGFTG 240
           PVVFKAHSGHMATAE+VA+AIIRAAE + MPAGVFNMI+G GVGEALVKHP I+ VGFTG
Sbjct: 181 PVVFKAHSGHMATAEQVANAIIRAAERSGMPAGVFNMIYGSGVGEALVKHPLIKGVGFTG 240

Query: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALKARAESVARDLTASVVQGCGQF 300
           SLKGGRALCDMAAARP+PIPVFAEMSSINPV++LP AL  RA+S+A DL ASVVQGCGQF
Sbjct: 241 SLKGGRALCDMAAARPEPIPVFAEMSSINPVVILPHALSRRADSIAHDLAASVVQGCGQF 300

Query: 301 CTNPGLVIGVASPEFTAFTQQVAQLIGDQPAQTMLNAGTLSSYGKGLEKLLAHPGIQHLA 360
           CTNPGLV+G+ S  FTAF  +VA L+ DQPAQTMLNAGTL SY  GL+ L AHPGI HLA
Sbjct: 301 CTNPGLVVGIRSDAFTAFQDRVAALMNDQPAQTMLNAGTLRSYAAGLQNLHAHPGIVHLA 360

Query: 361 GSQQAGNQAQPQLFKADVRLLIDGDEVLQEEVFGPTTVFVEVADQAQLSAALHGLHGQLT 420
           GS Q  +QAQPQLFKADV LL++GD+VLQEE+FGPT++F+EVADQAQLSAA++ L GQLT
Sbjct: 361 GSDQQAHQAQPQLFKADVELLLNGDKVLQEEIFGPTSIFIEVADQAQLSAAINALRGQLT 420

Query: 421 ATIIGEPADLQQFAELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480
           AT+IGEP DL QF ELT LLE KVGRIL+NGYPTGVEVCDSMVHGGPYPATSD+RGTSVG
Sbjct: 421 ATLIGEPEDLTQFTELTALLEMKVGRILINGYPTGVEVCDSMVHGGPYPATSDSRGTSVG 480

Query: 481 TLAIDRFLRPVCFQNYPDSLLPDALKNANPLRIQRLVDGTPSRDPL 526
           TLAIDRFLRPVCFQNYPD+LLPDALKNANPL I RLVDG  SRD L
Sbjct: 481 TLAIDRFLRPVCFQNYPDALLPDALKNANPLNISRLVDGCLSRDRL 526


Lambda     K      H
   0.319    0.135    0.392 

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: 901
Number of extensions: 25
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.

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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