GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruI in Pseudomonas fluorescens FW300-N2E2

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Pf6N2E2_5839 Glyoxylate carboligase (EC 4.1.1.47)

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5839
          Length = 588

 Score =  177 bits (448), Expect = 1e-48
 Identities = 149/494 (30%), Positives = 225/494 (45%), Gaps = 27/494 (5%)

Query: 30  LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPG-SGIRHVLTRHEQGAGFMADGYAR 88
           + A +A V ++   GVDT FGIPG     LY  L    GI HVL RH +GA  MA+GY R
Sbjct: 1   MRAIEAAVLVMRREGVDTAFGIPGAAINPLYSALQKVGGIDHVLARHVEGASHMAEGYTR 60

Query: 89  V-SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147
             +G  GVC   +GP  T++ T +  A ADS+P+L I+     A L K      +  D  
Sbjct: 61  TKAGNIGVCIGTSGPAGTDMVTGLYSASADSIPILCITGQAPRARLHKED---FQAVDIT 117

Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207
           ++  P+T ++   L P Q+P    +A+    S RP PV I +P DV  A +  D  A   
Sbjct: 118 SIVKPVTKWATTVLEPGQVPYAFQKAFFEMRSGRPGPVLIDLPFDVQMAEIEFDIDAYQP 177

Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGAL--AAGEALAALSERLAAPLFTSVAG 265
               +       +  A   L  A RP+L+AGGG +   A E L A +E    P+  ++ G
Sbjct: 178 LPLAKPAANRVQIEKALAMLNQAERPLLVAGGGIINADASELLVAFAELTGIPVIPTLMG 237

Query: 266 KGLLPPDAPL---NAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGE-LIR 321
            G +P D PL     G       G   + ++D+VL +G   A+       +   G   I 
Sbjct: 238 WGTIPDDHPLMVGMVGLQTSHRYGNATLLKSDVVLGIGNRWANRHTGSVDVYTEGRTFIH 297

Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALL--VRLPQEA-----RDS--APAAARVARLR 372
           VDI+P +    +   + +  DA   L   +   R  Q A     RD+       R A L+
Sbjct: 298 VDIEPTQIGRVFTPDLGIVSDAASALTVFIEVAREWQAAGKLKNRDAWLQDCQQRKASLQ 357

Query: 373 AEIRAAHAPLQALHQAILDRIAAALPAD-AFVST-DMTQLAYTGNYAFASRAPRSWLHPT 430
            +    + P++   Q + + +      D  +VST  ++Q+A  G        PR W++  
Sbjct: 358 RKTHFDNVPVKP--QRVYEEMNQVFGKDTCYVSTIGLSQIA--GAQFLHVYKPRHWINCG 413

Query: 431 GYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDA 490
             G LG+ +PA +G     P R  + L GD  F +  +ELA  + +   P + ++ NN  
Sbjct: 414 QAGPLGWTIPAALGVVKADPSRKVVALSGDYDFQFMIEELAVGA-QFKLPYIHVVVNNSY 472

Query: 491 LGQIRDDMLGLDIE 504
           LG IR    G D++
Sbjct: 473 LGLIRQAQRGFDMD 486


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: 703
Number of extensions: 43
Number of successful extensions: 6
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: 588
Length adjustment: 36
Effective length of query: 523
Effective length of database: 552
Effective search space:   288696
Effective search space used:   288696
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.

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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:

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