GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC 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)



>FitnessBrowser__Koxy:BWI76_RS10695
          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 (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