Alignments for a candidate for tynA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for tynA in Pseudomonas fluorescens GW456-L13

Align Primary amine oxidase; Monamine oxidase; Tyramine oxidase; EC 1.4.3.21 (characterized)
to candidate PfGW456L13_2439 Monoamine oxidase (1.4.3.4)

Query= SwissProt::P80695
         (752 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2439
          Length = 762

 Score = 1147 bits (2966), Expect = 0.0
 Identities = 540/750 (72%), Positives = 631/750 (84%), Gaps = 7/750 (0%)

Query: 5   SPRKTALA---LAVALSCA----WQSPAFAHGGEAHMVPMDKTLQDFGADVQWDDYAQMF 57
           SP++T LA   LA+ LS      W   A AHGG A MVP+   L++FGA V+WDDYA +F
Sbjct: 7   SPKRTPLARLALAITLSTLGLPFWAGNAQAHGGHAEMVPLQAGLEEFGATVKWDDYANLF 66

Query: 58  TLIKDGAYVKVKPGAKTAIVNGKTLELQVPVVMKDGKAWVSDTFINDVFQSGLDQTFQVE 117
           T+ KDG Y+KVKP +K A++NGK +EL VPVV KD  A++S  FIN VFQSGLD+TF VE
Sbjct: 67  TIAKDGVYLKVKPDSKVAMLNGKRIELTVPVVFKDHTAFMSKDFINQVFQSGLDKTFVVE 126

Query: 118 KRPHPLNSLSAAEISAAVAIVKAAADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAPR 177
            RP+PLN LSAAEI+ AV IVK + ++KP  RFTE+S++EP K  VW+FAL G  V  PR
Sbjct: 127 TRPNPLNPLSAAEITTAVDIVKKSENYKPGFRFTEVSVKEPPKDQVWNFALTGQNVAQPR 186

Query: 178 AADVIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAEVLK 237
            A +++LDGKHVIEA VDL  K++ SW PI+ AHGMVLLDDFA+VQ  +  S E+A+ L 
Sbjct: 187 QASIVVLDGKHVIEAQVDLDTKELKSWKPIEGAHGMVLLDDFATVQTAVETSPEYAQALA 246

Query: 238 KHGIDDPSKVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIENLVAVVDL 297
           K GI+D  KV+ TPLTVG+FDGKDGL QD RLLK+VSYL+ GDGNYWAHPIE LVA+VDL
Sbjct: 247 KRGINDVKKVVATPLTVGFFDGKDGLAQDKRLLKIVSYLNTGDGNYWAHPIEGLVAIVDL 306

Query: 298 EQKKIIKIEEGPTIPVPMAARPYDGRDRVAPKIKPLDIIEPEGKNYTITGDMIHWQNWDF 357
           EQKK+IKIE+   IPVPM   PYDGR R    +KPL+IIEPEGKNYTI+G+ IHWQNWDF
Sbjct: 307 EQKKLIKIEDDALIPVPMNPTPYDGRGRQGVAVKPLEIIEPEGKNYTISGNSIHWQNWDF 366

Query: 358 HLRMNSRVGPILSTVTYNDNGKKRQVMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMG 417
           H+R++SRVGPILSTVTY+D GKKR++MYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMG
Sbjct: 367 HVRLDSRVGPILSTVTYDDKGKKRKIMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMG 426

Query: 418 TLTSPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYAGPEYKHQEMGKPNVST 477
           TLTSPI RGKDAP NAVLLD TIADYTGTPT IPRA+A+FERYAGPEYKHQEMG+PN+ST
Sbjct: 427 TLTSPIARGKDAPQNAVLLDATIADYTGTPTAIPRAMAVFERYAGPEYKHQEMGQPNLST 486

Query: 478 ERRELVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGVQAKTMHDPSAKEDTR 537
           ERRELVVRWISTVGNYDYIFDWVF +NGTIGIDAGATGIEAVKGV++KTMH+ +A+EDTR
Sbjct: 487 ERRELVVRWISTVGNYDYIFDWVFQQNGTIGIDAGATGIEAVKGVKSKTMHEDTAREDTR 546

Query: 538 YGTLIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTAGGPRTSTMQINQYTI 597
           YGTL+DHNIVGTTHQHIYNFRLD+DVDGE N+LV ++P V PN  GGPRTSTMQ     +
Sbjct: 547 YGTLLDHNIVGTTHQHIYNFRLDMDVDGEQNSLVEVNPVVLPNDRGGPRTSTMQTETKVV 606

Query: 598 DSEQKAAQKFDPGTIRLLSNITKENRMGNPVSYQIIPYAGGTHPVATGAKFAPDEWIYHR 657
            +EQ+AAQKFDP T+RLL+N +KEN++GNPVSYQ+IPYAGGTHPVA GA F  DEW+YHR
Sbjct: 607 GNEQQAAQKFDPSTVRLLTNFSKENKVGNPVSYQLIPYAGGTHPVAKGANFGKDEWLYHR 666

Query: 658 LSFMDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQYAKDDESLDNHDDVVWITTGTTHV 717
           LSFMDKQLWVT+Y+P E++PEGKYPNRS  D+GLGQ+ +D+ S++N DDVVW+TTGTTH+
Sbjct: 667 LSFMDKQLWVTQYNPEEKYPEGKYPNRSDKDSGLGQFTQDNHSIENTDDVVWLTTGTTHI 726

Query: 718 ARAEEWPIMPTEWAHALLKPWNFFDETPTL 747
           ARAEEWPIMPTEW H LLKPWNFFDETPTL
Sbjct: 727 ARAEEWPIMPTEWVHVLLKPWNFFDETPTL 756


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: 2024
Number of extensions: 89
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: 762
Length adjustment: 40
Effective length of query: 712
Effective length of database: 722
Effective search space:   514064
Effective search space used:   514064
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources