GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Pseudomonas stutzeri RCH2

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF1235 Psest_1268 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>FitnessBrowser__psRCH2:GFF1235
          Length = 382

 Score =  172 bits (437), Expect = 1e-47
 Identities = 124/360 (34%), Positives = 182/360 (50%), Gaps = 13/360 (3%)

Query: 35  LLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVDAE- 93
           L LS G PDFD P  + +A    ++AG+  YA + G  ALR+++A +     G+ VDA  
Sbjct: 27  LNLSQGFPDFDGPEALREAVAGHVMAGHNQYAPMTGLPALREQVAAKVAGLYGRDVDAAA 86

Query: 94  QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFRV 153
           +V +  GA  A++  +Q ++ PGDEVIV +P Y +YE      G   +   + S   FR+
Sbjct: 87  EVTITPGATQAIFCAIQAVIRPGDEVIVFDPCYDSYEPSVQLAGGVCIHQQL-SLPDFRI 145

Query: 154 QAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLFD 213
             + +A  ITPRTR + LN+PHNPSGA +     + LA L    D++++SDEVY  L+FD
Sbjct: 146 DWQRLADAITPRTRMIVLNTPHNPSGALIDADDLDRLAALIRERDIYLLSDEVYEHLVFD 205

Query: 214 G-EHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPE 272
           G EH S      +  R   ++S  K++ +TGW+ G+VV P  L   L  +   + +    
Sbjct: 206 GREHASVLRHDELYQRAFVISSFGKTYHVTGWKTGYVVAPPMLSVELRKVHQYVSFTGVT 265

Query: 273 FIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVD---IR 329
            +Q A    + A    L  +   Y+ +RDL  + LA S      R  G  F + D   IR
Sbjct: 266 PLQWALADFMAAHPEHLAELPAFYQAKRDLFCDLLAGS-RFSFTRAAGTYFQLADYSAIR 324

Query: 330 PTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGA---EPLREACRRIALCA 386
           P  L   A A+ L   HGV+ +    F      ++RL     A   E LR+A  R  LCA
Sbjct: 325 P-DLDDVAMAEWLTREHGVACIPISVFYQHPPANLRLVRFCFAKREETLRQAAER--LCA 381


Lambda     K      H
   0.322    0.136    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: 434
Number of extensions: 34
Number of successful extensions: 4
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: 393
Length of database: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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