GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N1B4

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Pf1N1B4_3024 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)

Query= SwissProt::Q8ZPV0
         (492 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3024
          Length = 474

 Score =  194 bits (494), Expect = 4e-54
 Identities = 155/469 (33%), Positives = 227/469 (48%), Gaps = 22/469 (4%)

Query: 3   LWINGDWITGQGERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQ 62
           L ING  + G G  +   NP    +L + N+A+ AQV  A +AA  AF  W++     R 
Sbjct: 5   LLINGQLVNGDGPAQAVFNPALGRVLVEINEASEAQVDAAVRAADNAFQAWSQTTPKERS 64

Query: 63  AIVEKFAALLEAHKAELTEVIARETGKPRWEAAT-EVTAMINKIAISIKAYHARTGAQKS 121
            ++ K A ++EAH  EL ++ +   GKP   A   E+ A+ +       A    +GA   
Sbjct: 65  LLLLKLADIIEAHGEELAKLESDNCGKPYSAALNDEIPAIADVFRFFAGANRCMSGALGG 124

Query: 122 ELVDG-AATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETV 180
           E + G  + +R  P GV+A   P+N+P  +    I PAL AGNT++ KPSE TP    T 
Sbjct: 125 EYLPGHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPL---TA 181

Query: 181 IKLWERAG--LPAGVLNLVQG-GRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPE 237
           ++L E A    PAGVLNLV G G   G AL +   +  +  TGS +TG  +    +G  +
Sbjct: 182 LRLAELASDIFPAGVLNLVYGRGSAVGTALVNHPKVRMVSLTGSIATGSNIISSTAGNVK 241

Query: 238 KILALEMGGNNPLIIEDAANIDAAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLAR 297
           + L +E+GG  P+II D A+IDAAV       F  AGQ CT A R+  + G   D F+ +
Sbjct: 242 R-LHMELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIY-DQFVEK 299

Query: 298 LVDVAGRLQPGRWDDDPQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTSL 357
           L      ++ G   DDP   +G LISAQ    V     +  A     L+   K  EG   
Sbjct: 300 LGAAVSSIKYG-LQDDPSTELGPLISAQHRDRVTALVERAMAQPHIRLITGGKAVEGNGF 358

Query: 358 LTPGIIELTGVADVPDE------EVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTD 411
                 E T +ADV  +      EVFGP+++V R+    +A+  AN++ +GL+  + +TD
Sbjct: 359 ----FFEPTVLADVQQDDEIVRREVFGPVVSVTRFTDEAQALAWANDSDYGLASSVWTTD 414

Query: 412 RAQFEQLLLEARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWYAAD 460
             +  +L    + G   W        S  P GG   SG  +  + Y  +
Sbjct: 415 VGRAHRLSARLQYG-CTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLE 462


Lambda     K      H
   0.319    0.134    0.411 

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: 590
Number of extensions: 25
Number of successful extensions: 6
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: 492
Length of database: 474
Length adjustment: 34
Effective length of query: 458
Effective length of database: 440
Effective search space:   201520
Effective search space used:   201520
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 (21.7 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