GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Herbaspirillum seropedicae SmR1

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate HSERO_RS05635 HSERO_RS05635 hypothetical protein

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05635 HSERO_RS05635
           hypothetical protein
          Length = 458

 Score =  306 bits (784), Expect = 9e-88
 Identities = 172/451 (38%), Positives = 254/451 (56%), Gaps = 10/451 (2%)

Query: 9   KTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVG 68
           +T    AL R H + P T  ++  E G  I+   +G Y+ D +  ++LDA +GLWCVN G
Sbjct: 2   QTSALAALDRRHLIHPVTSLREHEELGPLILKSGQGAYLTDHQDKQLLDAFSGLWCVNTG 61

Query: 69  YGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEAND 128
           YG+E +++AAT QM+ LP+   +F  A  P + LAK + D++P  + HV+FT  GS+A D
Sbjct: 62  YGQESVIRAATEQMQRLPYATGYFHFASEPAILLAKKLVDISPASLQHVYFTLGGSDAVD 121

Query: 129 TVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQ 188
             +R + HY  + G+P K+  I    GYHGS+  G  L  +   H   + P+P   ++  
Sbjct: 122 AAIRYITHYHHSIGKPGKQHFISLQRGYHGSSSVGAGLTALPNFHYHFNLPLPTQHYLPS 181

Query: 189 PYWYGEGGDMSPDEFGVWAAEQ-LEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPK 247
           PY Y    ++  DE  + A+ Q L  K+ E+G +NVAAF  EPIQG+GGV+VPP  +   
Sbjct: 182 PYPY--RSELQGDEAIIAASVQALRDKVAELGADNVAAFFCEPIQGSGGVVVPPKGWLKA 239

Query: 248 IREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRD 307
           ++    + DILF+ DEVI GFGRTG  F        PDLM +AKGLT+GY PMG V++ D
Sbjct: 240 MQLACNELDILFVVDEVITGFGRTGPMFACLDEDVQPDLMTMAKGLTAGYAPMGAVMMSD 299

Query: 308 EIVEVLNQGGEFY----HGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRW 363
            +   +  G        HG TYS HPV+AAVALE +R+  E  +++  +    P      
Sbjct: 300 RVYNGIADGAPMSTVVGHGQTYSAHPVSAAVALEVLRLYEEGGLLDNGR-RLEPVFAGGL 358

Query: 364 QELADHPLVGEARGVGMVAALELVKNKKTRERFT-DKGVGMLCREHCFRNGLIMRAVGDT 422
           + L  HPLVG+AR  G++ ALELV +K+T+ RF  +  +     +  +R+GL+ RA GD 
Sbjct: 359 RALLAHPLVGDARSRGLLGALELVADKQTKARFAPELKLHDRIFQAAYRHGLVFRAFGDN 418

Query: 423 MI-ISPPLVIDPSQIDELITLARKCLDQTAA 452
           ++  +P L         +    +  LD+  A
Sbjct: 419 ILGFAPALCYTQEDFALMFARLKAILDEVLA 449


Lambda     K      H
   0.320    0.138    0.425 

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: 562
Number of extensions: 24
Number of successful extensions: 5
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: 456
Length of database: 458
Length adjustment: 33
Effective length of query: 423
Effective length of database: 425
Effective search space:   179775
Effective search space used:   179775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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