Alignments for a candidate for aruI in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for aruI in Pseudomonas fluorescens FW300-N2E3

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate AO353_03865 AO353_03865 hypothetical protein

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03865
          Length = 545

 Score =  435 bits (1118), Expect = e-126
 Identities = 257/542 (47%), Positives = 332/542 (61%), Gaps = 23/542 (4%)

Query: 31  TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90
           T G+ LV+LL  YGV+ VFGIPGVHT+ELYRGL  S I HV  RHEQGAGFMADGYAR S
Sbjct: 3   TCGEVLVKLLEGYGVEQVFGIPGVHTVELYRGLARSSINHVTPRHEQGAGFMADGYARTS 62

Query: 91  GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150
           GKPGVCF+ITGPG+TN+ TA+GQAYADS+P+LVISSV     LG G G LHE  +Q A+ 
Sbjct: 63  GKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRNQLGGGRGKLHELPNQSALV 122

Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRP 210
           A + AFS   +S  +LP ++ARA+A+F + RPRPVHI IPLDVL      D  A +A +P
Sbjct: 123 AGVAAFSHTLMSAAELPGVLARAFALFQAGRPRPVHIEIPLDVL----VEDADALLASQP 178

Query: 211 ---GRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKG 267
               R      A+   +E LA A+RP+++AGGG++ A   L  L+E L AP+  ++  KG
Sbjct: 179 VNITRAGAAPSAVAQMSELLANAKRPLILAGGGSIDAAAELTRLAELLDAPVALTINAKG 238

Query: 268 LLPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDF---WRERLPLSGELIRVDI 324
           +LP   PL  G++  +     ++A+AD+VLA+GTE+A+TD+   +     + G L+RVDI
Sbjct: 239 MLPSAHPLLIGSTQTLVATRALVADADVVLAIGTELAETDYDVTFAGGFEIPGTLLRVDI 298

Query: 325 DPRKFNDFYPSAVALRGDARQTLEALLVRLPQEA---RDSAPAAARVARLRAEIRAA-HA 380
           D  +    YP  VAL  DA+   +ALL  + + +   R S    AR A LRAE+     A
Sbjct: 299 DSDQTVRNYPPKVALVSDAQSAAQALLDGVAKHSLAERCSDWGQARAASLRAELETIWDA 358

Query: 381 PLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGYGL 439
           P +A     L  +   LP   FV  D TQ  YTGN  F    PR W +  TGYGTLGY L
Sbjct: 359 PTRA-QTLFLQTVQDELPEAVFVG-DSTQPVYTGNLTFNPERPRRWFNSSTGYGTLGYAL 416

Query: 440 PAGIGAKLGAPQR-----PGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQI 494
           PA IGA LG  Q      P + L+GDGG  +T  ELA+A  E  +P++VLLWNN    +I
Sbjct: 417 PAAIGAWLGGGQERNSRPPVVCLIGDGGLQFTLPELASA-VEARTPVIVLLWNNQGYEEI 475

Query: 495 RDDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIELR 554
           +  M+  DIEPVGV    PDF  + +  GCA      ++EL   LRA   + G TLIE+ 
Sbjct: 476 KKYMVNRDIEPVGVDIYTPDFIAVAKGLGCAAHAVSGVEELRAALRAATDRQGPTLIEID 535

Query: 555 HA 556
            A
Sbjct: 536 QA 537


Lambda     K      H
   0.321    0.136    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: 810
Number of extensions: 31
Number of successful extensions: 8
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: 559
Length of database: 545
Length adjustment: 36
Effective length of query: 523
Effective length of database: 509
Effective search space:   266207
Effective search space used:   266207
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: 53 (25.0 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