GapMind for catabolism of small carbon sources

 

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

Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate Pf6N2E2_2163 Lysine 2,3-aminomutase (EC 5.4.3.2)

Query= SwissProt::Q9XBQ8
         (416 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2163
          Length = 465

 Score =  226 bits (576), Expect = 1e-63
 Identities = 137/362 (37%), Positives = 202/362 (55%), Gaps = 27/362 (7%)

Query: 4   RRYELFKDVSDADWNDWRWQVRNRIETVEELKKYIP------LTKEEEEGVAQCVKSLRM 57
           R  + +KD+    + +  WQ +N I +V  L   I         ++ EEG      S+R+
Sbjct: 45  RDLDHWKDIDVELFLNHLWQEKNAITSVGALGALIKNRISAAFLRDLEEGHQMAPMSIRL 104

Query: 58  AITPYYLSLIDPNDPN-DPVRKQAIPTALELNKAAADLE-DPLHEDTDSPVPGLTHRYPD 115
             TPY LSLID ++P  DP+R+Q +P A E++     ++ DP+ E  DSP PGLTHRYPD
Sbjct: 105 --TPYILSLIDWDNPYLDPLRRQFLPLASEISIDHPMVKLDPMGEQDDSPAPGLTHRYPD 162

Query: 116 RVLLLITDMCSMYCRHCTRRRFAGQSDDSM-------PMERIDKAIDYIRNTPQVRDVLL 168
           RVL L T++C +YCR+CTR    G   D++       P ER + A+ YI     V DV++
Sbjct: 163 RVLFLATNVCPVYCRYCTRSYAVGLDTDAVTKKKINAPGERWEPALRYIETNSSVEDVVI 222

Query: 169 SGGDALLVSDETLEYIIAKLREIPHVEIVRIGSRTPVVLPQRITPE---------LVNML 219
           SGGDA  +    +  I  +L ++PHV  +R  ++   VLP +I  +         L +  
Sbjct: 223 SGGDAYRLKARQITEIGERLLDVPHVRRMRFATKGLAVLPMKIQSDHDWTDAISRLSDRA 282

Query: 220 KKYHP-VWLNTHFNHPNEITEESTRACQLLADAGVPLGNQSVLLRGVNDCVHVMKELVNK 278
           +K H  + ++THFNHPNEIT  + +A  +L + GV + NQ+V+L+GVND    M  L   
Sbjct: 283 RKVHKSIAIHTHFNHPNEITAVTAKALGMLYERGVEVRNQAVILKGVNDNPQTMHRLNEC 342

Query: 279 LVKIRVRPYYIYQCDLSLGLEHFRTPVSKGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKT 338
           L  + VRPYY +Q D+  G+E  RT +   I + +  RG  +G+  P F+VD PGGGGK 
Sbjct: 343 LAYLNVRPYYCFQGDMIRGVEALRTSLCDSIALEKSTRGLIAGHNTPHFIVDLPGGGGKR 402

Query: 339 PV 340
            +
Sbjct: 403 DI 404


Lambda     K      H
   0.320    0.138    0.422 

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: 531
Number of extensions: 25
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: 416
Length of database: 465
Length adjustment: 32
Effective length of query: 384
Effective length of database: 433
Effective search space:   166272
Effective search space used:   166272
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 (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