GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Klebsiella michiganensis M5al

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS10695 BWI76_RS10695 aldehyde
           dehydrogenase PuuC
          Length = 495

 Score =  824 bits (2129), Expect = 0.0
 Identities = 405/495 (81%), Positives = 444/495 (89%)

Query: 1   MNFHHLAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDID 60
           M+FH+LAYWQ KA  L IE RLFINGEY+AAA+N  F T+DP  Q  LA++ARGK  D+D
Sbjct: 1   MDFHNLAYWQQKARELTIETRLFINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVD 60

Query: 61  RAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDD 120
           RA+ AARGVF+RGDWS +SPA+RKAVL K ADLM+AH EELALLETLDTGKPIRHSLRDD
Sbjct: 61  RAVQAARGVFDRGDWSQASPAQRKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDD 120

Query: 121 IPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGP 180
           IPGAARAIRWYAEAIDKVYGEVA T  +ELAMIVREP+GVIAA+VPWNFPLLL CWKLGP
Sbjct: 121 IPGAARAIRWYAEAIDKVYGEVAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGP 180

Query: 181 ALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAI 240
           ALA+GNSV+LKPSEKSPL+A+RLAGLAK+AGLPDGV NVV+GFGHEAGQAL+ H D++ I
Sbjct: 181 ALASGNSVVLKPSEKSPLTALRLAGLAKQAGLPDGVFNVVSGFGHEAGQALALHPDVEVI 240

Query: 241 AFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQ 300
            FTGSTRT KQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQ+A +ATA GIFYNQGQ
Sbjct: 241 TFTGSTRTAKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQ 300

Query: 301 VCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREG 360
           VCIAGTRLLLEESIAD FL LLK+QA+ WQPG+PLDP TTMG LID  HADSVHSFIR G
Sbjct: 301 VCIAGTRLLLEESIADRFLDLLKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAG 360

Query: 361 ESKGQLLLDGRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLAND 420
           E+   LLLDGR     AA+GPTIFVDVDP + LS+EEIFGPVLVVTRF +EEQAL LAND
Sbjct: 361 EAHSTLLLDGRKNPWPAAVGPTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALAND 420

Query: 421 SQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL 480
           S+YGLGAAVWTRDLSRAHR+SRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL
Sbjct: 421 SRYGLGAAVWTRDLSRAHRVSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL 480

Query: 481 EKFTELKTIWISLEA 495
           EKFTELKTIWI+LE+
Sbjct: 481 EKFTELKTIWIALES 495


Lambda     K      H
   0.317    0.133    0.389 

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: 767
Number of extensions: 11
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: 495
Length of database: 495
Length adjustment: 34
Effective length of query: 461
Effective length of database: 461
Effective search space:   212521
Effective search space used:   212521
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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