GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpaH in Klebsiella michiganensis M5al

Align Anthranilate 3-monooxygenase oxygenase component; 4-hydroxyphenylacetate 3-monooxygenase oxygenase component; 4 HPA 3-hydroxylase; Anthranilate 3-hydroxylase; Anthranilate hydroxylase; EC 1.14.14.8; EC 1.14.14.9 (characterized)
to candidate BWI76_RS03830 BWI76_RS03830 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component

Query= SwissProt::A4IT51
         (494 letters)



>FitnessBrowser__Koxy:BWI76_RS03830
          Length = 520

 Score =  233 bits (594), Expect = 1e-65
 Identities = 155/486 (31%), Positives = 248/486 (51%), Gaps = 17/486 (3%)

Query: 7   TGAQYISGLKSRKPEIWLSGRRVINVCEEPVFKQPIREIARLYDMQHDPEYQDKITH-IC 65
           TG +Y+  L+  + EI++ G RV +V   P F+     +A++YD  H PE QD +     
Sbjct: 15  TGEEYLKSLQDGR-EIYIYGERVKDVTTHPAFRNAAASVAQMYDALHKPELQDTLCWGTD 73

Query: 66  TETGERVSNAFLVPKSREDLLARRALFEVWARATFGLMGRTPDFLNVVLTSLYSNASFLE 125
           T +G      F V KS +DL  +R     W+R ++G MGRTPD+      +L +N  F  
Sbjct: 74  TGSGGYTHKFFRVAKSADDLRQQRDAIAEWSRLSYGWMGRTPDYKAAFGCALGANPGFYG 133

Query: 126 KYNPQWAENIRAYYRYVRDNDLFLTHAIINPQNDRSKPSHEQQDTFTHLGVVRETPEGLI 185
               Q+ +N R +Y  +++  L+  HAI+NP  DR KP+ E +D +  L   +ET  G+I
Sbjct: 134 ----QFEQNARDWYTRIQETGLYFNHAIVNPPIDRHKPADEVKDVYIKLE--KETDAGII 187

Query: 186 VRGAKMLATLAPITDEVIIYTFPGYKPGDER-YAVSFAIPIDTPGLRILCR---EPMQDG 241
           V GAK++AT + +T   +I        G+   +A+ F  P+D  G++++ R   E +   
Sbjct: 188 VSGAKVVATNSALTHYNMIGFGSAQVMGENPDFALMFVAPMDAEGVKLISRASYELVAGA 247

Query: 242 TRPLFDHPLASRFEEMDALLVFNDVLVPWDRVFIYNNVEAANLLYPKTGIAQQPAHQTGV 301
           T   +D+PL+SRF+E DA+LV ++VL+PW+ V IY + +       + G A+    Q  V
Sbjct: 248 TGSPYDYPLSSRFDENDAILVMDNVLIPWENVLIYRDFDRCRRWTMEGGFARMYPLQACV 307

Query: 302 RGLIKLQFATEVAIRLADSIGVDVYLNVQNDLGELLQSVEAIRALLHLAEHELEVLPSGE 361
           R  +KL F T +  R  +  G   +  VQ +LGE++       AL      E     +G 
Sbjct: 308 RLAVKLDFITALLKRSLECTGTLEFRGVQAELGEVVAWRNMFWALSDSMCAEATPWVNGA 367

Query: 362 VMPGWVPLETIRGLLPKLYPRAVEVLQIIGAGGLLMSPTGA-DFANPELAADMEKYYAGR 420
            +P    L+T R + P  Y +   +++     GL+  P+ A D  NP++   + KY  G 
Sbjct: 368 YLPDHAALQTYRVMAPMAYAKIKNIIERSVTSGLIYLPSSARDLNNPQINEYLAKYVRGS 427

Query: 421 IGVGGEERVRLFKLAWDLCGEAFGQRLLQYERFYTG--DPIRKRAI--FYNNIKRERTLV 476
            G+   ER+++ KL WD  G  FG R   YE  Y+G  D IR + +    ++   ++ + 
Sbjct: 428 NGMDHVERIKILKLMWDAIGSEFGGRHELYEINYSGSQDEIRLQCLRQAQSSGNMDKMMA 487

Query: 477 MVDEAL 482
           MVD  L
Sbjct: 488 MVDRCL 493


Lambda     K      H
   0.322    0.139    0.418 

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: 586
Number of extensions: 41
Number of successful extensions: 7
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: 494
Length of database: 520
Length adjustment: 34
Effective length of query: 460
Effective length of database: 486
Effective search space:   223560
Effective search space used:   223560
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: 52 (24.6 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