GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Pseudomonas fluorescens FW300-N2C3

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AO356_27465 AO356_27465 ketoglutarate semialdehyde dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_27465
          Length = 526

 Score =  830 bits (2144), Expect = 0.0
 Identities = 412/526 (78%), Positives = 463/526 (88%)

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

Query: 61  ALSAARRAQFLDAVADELDALGDEFVELVCRETALPAARIKGERGRTSGQMRLFATVLRR 120
            LSA +RA+FLDA+A ELDAL DEF+ LVCRETALP ARI+GER RTSGQMRLFA VLRR
Sbjct: 61  TLSANKRAEFLDAIAQELDALDDEFIALVCRETALPVARIQGERARTSGQMRLFANVLRR 120

Query: 121 GDFYGARIDKALPDRQPMPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC 180
           GDFYGARID+ALP R P+PRPDLRQYR  +GPVAVFGASNFPLAFSTAGGDTA+ALAAGC
Sbjct: 121 GDFYGARIDQALPLRTPLPRPDLRQYRTAIGPVAVFGASNFPLAFSTAGGDTASALAAGC 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 SLKGGRALCDMAAARPEPIPVFAEMSSINPVVILPEALSRRADSIAHDLAASVVQGCGQF 300

Query: 301 CTNPGLVIGVASPEFTAFTQQVAQLIGDQPAQTMLNAGTLSSYGKGLEKLLAHPGIQHLA 360
           CTNPGLV+G+ S  FTAF  +VA L+ DQPAQTMLN+GTL SY  GL+ L AHPGI HLA
Sbjct: 301 CTNPGLVVGIRSGAFTAFQDRVAALMNDQPAQTMLNSGTLRSYAAGLQNLHAHPGIVHLA 360

Query: 361 GSQQAGNQAQPQLFKADVRLLIDGDEVLQEEVFGPTTVFVEVADQAQLSAALHGLHGQLT 420
           GS Q G+QAQPQLFKADV LL +GD+VLQEE+FGPT++F+EVADQAQL+AA++ LHGQLT
Sbjct: 361 GSDQQGHQAQPQLFKADVALLFNGDKVLQEEIFGPTSIFIEVADQAQLNAAINALHGQLT 420

Query: 421 ATIIGEPADLQQFAELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480
           AT+IGEP DL QFAELT LLE KVGRIL+NGYPTGVEVCDSMVHGGPYPATSD+RGTSVG
Sbjct: 421 ATLIGEPEDLTQFAELTALLETKVGRILINGYPTGVEVCDSMVHGGPYPATSDSRGTSVG 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: 910
Number of extensions: 26
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:

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