Alignments for a candidate for tynA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for tynA in Herbaspirillum seropedicae SmR1

Align primary-amine oxidase (EC 1.4.3.21) (characterized)
to candidate HSERO_RS17625 HSERO_RS17625 tyramine oxidase

Query= BRENDA::P46883
         (757 letters)



>FitnessBrowser__HerbieS:HSERO_RS17625
          Length = 748

 Score = 1068 bits (2763), Expect = 0.0
 Identities = 509/745 (68%), Positives = 597/745 (80%), Gaps = 1/745 (0%)

Query: 12  TTLALAVALSFAWQAPVFAHGGEAHMVPMDKTLKEFGADVQWDDYAQLFTLIKDGAYVKV 71
           T  A  ++ +     P  AHG  AHM+P+ KT+++FGA V+WD YA L+T+ ++   V+V
Sbjct: 3   TLTAAGLSTALLGPLPAAAHGAAAHMLPLKKTMEDFGATVRWDAYAGLWTIQRNSVTVRV 62

Query: 72  KPGAQTAIVNGQPLALQVPVVMKDNKAWVSDTFINDVFQSGLDQTFQVEKRPHPLNALTA 131
           KP A TA+VNGQ + L VP+VMK  + +VSD FIN VF   LD+TFQ+E  PHPLN L+A
Sbjct: 63  KPRATTALVNGQSVKLPVPLVMKGGQPYVSDEFINTVFAPSLDKTFQIEAVPHPLNPLSA 122

Query: 132 DEIKQAVEIVKASADFKPNTRFTEISLLPPDKEAVWAFALENKPVDQPRKADVIMLDGKH 191
           DEI  A+E++KAS  ++PN RFTEI+L  P KE VW FAL  +     R+AD  +LDG  
Sbjct: 123 DEINAALEVLKASGRWQPNYRFTEITLAEPPKEQVWKFALGERGQTIARRADFTLLDGSK 182

Query: 192 IIEAVVDLQNNKLLSWQPIKDAHGMVLLDDFASVQNIINNSEEFAAAVKKRGITDAKKVI 251
           +IE  VDL    +  W+P +  HGMVL+DDFA+VQN + +S E+A A+ KRGITD KKV+
Sbjct: 183 VIEGTVDLGQRNVTRWEPKEGVHGMVLVDDFATVQNAMESSPEYAQALAKRGITDIKKVV 242

Query: 252 TTPLTVGYFDGKDGLKQDARLLKVISYLDVGDGNYWAHPIENLVAVVDLEQKKIVKIEEG 311
            TPLTVGYF GKD L++DARLLKV+SYLDVGDGNYWAHPIENLVAVVDL QKK++KIE+ 
Sbjct: 243 ATPLTVGYFGGKDALQEDARLLKVVSYLDVGDGNYWAHPIENLVAVVDLVQKKVIKIEDN 302

Query: 312 PVVPVPMTARPFDGRDR-VAPAVKPMQIIEPEGKNYTITGDMIHWRNWDFHLSMNSRVGP 370
            V+PVPM    +DG  R + P  KP+ I EPEGKNYTITG+ + WRNW+ H  ++SRVG 
Sbjct: 303 GVIPVPMKPTGYDGSGRALVPPPKPLDISEPEGKNYTITGNTLRWRNWEMHFKLDSRVGL 362

Query: 371 MISTVTYNDNGTKRKVMYEGSLGGMIVPYGDPDIGWYFKAYLDSGDYGMGTLTSPIARGK 430
           M STVTYND+G KR++MYEGSLGGMIVPYGDPD+GWYFKAYLDSG+YGMGTLTSPI RGK
Sbjct: 363 MFSTVTYNDHGKKRQIMYEGSLGGMIVPYGDPDVGWYFKAYLDSGEYGMGTLTSPIERGK 422

Query: 431 DAPSNAVLLNETIADYTGVPMEIPRAIAVFERYAGPEYKHQEMGQPNVSTERRELVVRWI 490
           DAP N VLL+ T+AD +G P  IPRAI VFERYAGPE+KHQE GQPN+S ERRELV+RWI
Sbjct: 423 DAPDNVVLLDATLADTSGKPRTIPRAIGVFERYAGPEFKHQEYGQPNLSVERRELVIRWI 482

Query: 491 STVGNYDYIFDWIFHENGTIGIDAGATGIEAVKGVKAKTMHDETAKDDTRYGTLIDHNIV 550
           STVGNYDYIFDW+F ENGTIGI+AGATGIEAVKGVK+ TM D +A +DTRYGTLIDHNIV
Sbjct: 483 STVGNYDYIFDWVFAENGTIGINAGATGIEAVKGVKSSTMRDASAAEDTRYGTLIDHNIV 542

Query: 551 GTTHQHIYNFRLDLDVDGENNSLVAMDPVVKPNTAGGPRTSTMQVNQYNIGNEQDAAQKF 610
           GTTHQHIYNFRLDLDVDG+NNSL  +DPVV PNT GGPR+STMQ  Q     EQ AAQKF
Sbjct: 543 GTTHQHIYNFRLDLDVDGQNNSLTEVDPVVLPNTPGGPRSSTMQTVQRTAETEQQAAQKF 602

Query: 611 DPGTIRLLSNPNKENRMGNPVSYQIIPYAGGTHPVAKGAQFAPDEWIYHRLSFMDKQLWV 670
           D  TIRLLSNPNK N++GNPVSYQ+IPYAGGTHP+AKGA F+PDEW+  RLSFMD+QLWV
Sbjct: 603 DASTIRLLSNPNKFNKVGNPVSYQLIPYAGGTHPIAKGANFSPDEWLNKRLSFMDRQLWV 662

Query: 671 TRYHPGERFPEGKYPNRSTHDTGLGQYSKDNESLDNTDAVVWMTTGTTHVARAEEWPIMP 730
           TRY P +RFPEGKYPNRS  DTGLG + KDN+S+ N D VVW+TTGTTHVARAEEWPIMP
Sbjct: 663 TRYDPQQRFPEGKYPNRSHEDTGLGAFVKDNQSIVNQDDVVWLTTGTTHVARAEEWPIMP 722

Query: 731 TEWVHTLLKPWNFFDETPTLGALKK 755
           TEWVH LLKPWNFFDETPTLG  KK
Sbjct: 723 TEWVHVLLKPWNFFDETPTLGLNKK 747


Lambda     K      H
   0.317    0.135    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: 1886
Number of extensions: 85
Number of successful extensions: 2
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: 757
Length of database: 748
Length adjustment: 40
Effective length of query: 717
Effective length of database: 708
Effective search space:   507636
Effective search space used:   507636
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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