GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tynA in Klebsiella michiganensis M5al

Align Primary amine oxidase; Monamine oxidase; Tyramine oxidase; EC 1.4.3.21 (characterized)
to candidate BWI76_RS13080 BWI76_RS13080 tyramine oxidase

Query= SwissProt::P80695
         (752 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS13080 BWI76_RS13080 tyramine
           oxidase
          Length = 752

 Score = 1524 bits (3946), Expect = 0.0
 Identities = 740/752 (98%), Positives = 745/752 (99%)

Query: 1   MAILSPRKTALALAVALSCAWQSPAFAHGGEAHMVPMDKTLQDFGADVQWDDYAQMFTLI 60
           MAILSPRKTALALAVAL CAWQSPAFAHGGEAHMVPMDKTLQDFG DVQWDDYAQMFTLI
Sbjct: 1   MAILSPRKTALALAVALFCAWQSPAFAHGGEAHMVPMDKTLQDFGVDVQWDDYAQMFTLI 60

Query: 61  KDGAYVKVKPGAKTAIVNGKTLELQVPVVMKDGKAWVSDTFINDVFQSGLDQTFQVEKRP 120
           KDGAYVKVKPGAKTAIVNGKTLELQVPVVMKDGKAWVSDTFINDVFQSGLDQTFQVEKRP
Sbjct: 61  KDGAYVKVKPGAKTAIVNGKTLELQVPVVMKDGKAWVSDTFINDVFQSGLDQTFQVEKRP 120

Query: 121 HPLNSLSAAEISAAVAIVKAAADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAPRAAD 180
           HPLNSLSAAEISAAVAIVKAAADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAPR AD
Sbjct: 121 HPLNSLSAAEISAAVAIVKAAADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAPRTAD 180

Query: 181 VIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAEVLKKHG 240
           VIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAEVLKKHG
Sbjct: 181 VIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAEVLKKHG 240

Query: 241 IDDPSKVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIENLVAVVDLEQK 300
           IDDPSKVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIENLVAVVDLEQK
Sbjct: 241 IDDPSKVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIENLVAVVDLEQK 300

Query: 301 KIIKIEEGPTIPVPMAARPYDGRDRVAPKIKPLDIIEPEGKNYTITGDMIHWQNWDFHLR 360
           KIIKIEEGPTIPVPMAARPYDGRDRVAP +KPL+IIEPEGKNYTITGDMIHW+NWDFHLR
Sbjct: 301 KIIKIEEGPTIPVPMAARPYDGRDRVAPTVKPLEIIEPEGKNYTITGDMIHWRNWDFHLR 360

Query: 361 MNSRVGPILSTVTYNDNGKKRQVMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMGTLT 420
           MNSRVGPILSTVT+NDNGKKRQVMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMGTLT
Sbjct: 361 MNSRVGPILSTVTWNDNGKKRQVMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMGTLT 420

Query: 421 SPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYAGPEYKHQEMGKPNVSTERR 480
           SPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYAGPEYKH EMGKPNVSTERR
Sbjct: 421 SPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYAGPEYKHLEMGKPNVSTERR 480

Query: 481 ELVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGVQAKTMHDPSAKEDTRYGT 540
           ELVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGVQAKTMHDPSAKEDTRYGT
Sbjct: 481 ELVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGVQAKTMHDPSAKEDTRYGT 540

Query: 541 LIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTAGGPRTSTMQINQYTIDSE 600
           LIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTAGGPRTSTMQINQYTI SE
Sbjct: 541 LIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTAGGPRTSTMQINQYTIASE 600

Query: 601 QKAAQKFDPGTIRLLSNITKENRMGNPVSYQIIPYAGGTHPVATGAKFAPDEWIYHRLSF 660
           QKAAQKFDPGTIRLLSN TKENRMGNPVSYQIIPYAGGTHPVATGAKFAPDEWIYHRLSF
Sbjct: 601 QKAAQKFDPGTIRLLSNTTKENRMGNPVSYQIIPYAGGTHPVATGAKFAPDEWIYHRLSF 660

Query: 661 MDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQYAKDDESLDNHDDVVWITTGTTHVARA 720
           MDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQYAKDDESLDNHDDVVWITTGTTHVARA
Sbjct: 661 MDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQYAKDDESLDNHDDVVWITTGTTHVARA 720

Query: 721 EEWPIMPTEWAHALLKPWNFFDETPTLGEKKE 752
           EEWPIMPTEWAHALLKPWNFFDETPTLGEKK+
Sbjct: 721 EEWPIMPTEWAHALLKPWNFFDETPTLGEKKQ 752


Lambda     K      H
   0.317    0.135    0.412 

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: 2346
Number of extensions: 104
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: 752
Length of database: 752
Length adjustment: 40
Effective length of query: 712
Effective length of database: 712
Effective search space:   506944
Effective search space used:   506944
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 (21.6 bits)
S2: 55 (25.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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