GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Pseudomonas fluorescens FW300-N2E2

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= reanno::WCS417:GFF827
         (481 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3298
          Length = 481

 Score =  916 bits (2367), Expect = 0.0
 Identities = 458/481 (95%), Positives = 474/481 (98%)

Query: 1   MSQAQRFDNYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWS 60
           ++ ++RFDNYINGQWVAGADYC N+NPS+LSDVIGEYAKAD  QVNAAI+AARAAFPAWS
Sbjct: 1   VADSKRFDNYINGQWVAGADYCTNINPSDLSDVIGEYAKADAAQVNAAIEAARAAFPAWS 60

Query: 61  TSGIQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120
           TSGIQARHDALDKVGSEILARREELG LLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR
Sbjct: 61  TSGIQARHDALDKVGSEILARREELGQLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120

Query: 121 LSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELV 180
           LSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELV
Sbjct: 121 LSGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELV 180

Query: 181 PGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSC 240
           PGCAWALAEIISRAGFPAG FNLVMGSGRVVGD+LVNSPKVDGISFTGSVGVGRQIAV+C
Sbjct: 181 PGCAWALAEIISRAGFPAGAFNLVMGSGRVVGDILVNSPKVDGISFTGSVGVGRQIAVNC 240

Query: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQF 300
           VSRQAKVQLEMGGKNPQIILDDADLKQAVEL+VQSAFYSTGQRCTASSRLIVTAGIHD+F
Sbjct: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELAVQSAFYSTGQRCTASSRLIVTAGIHDKF 300

Query: 301 VAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDT 360
           VAAMAERM+SIKVGHALK+GTDIGPVVS+AQL QDLKYIDIGQSEGARLVSGGGLVTCDT
Sbjct: 301 VAAMAERMQSIKVGHALKAGTDIGPVVSEAQLSQDLKYIDIGQSEGARLVSGGGLVTCDT 360

Query: 361 EGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL 420
           EGY+LAPTLFADSEA+MRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL
Sbjct: 361 EGYFLAPTLFADSEASMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSL 420

Query: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480
           KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG
Sbjct: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480

Query: 481 S 481
           S
Sbjct: 481 S 481


Lambda     K      H
   0.318    0.134    0.390 

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: 876
Number of extensions: 21
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: 481
Length of database: 481
Length adjustment: 34
Effective length of query: 447
Effective length of database: 447
Effective search space:   199809
Effective search space used:   199809
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: 51 (24.3 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