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_RS15105 BWI76_RS15105 4-hydroxyphenylacetate 3-monooxygenase oxygenase component

Query= SwissProt::A4IT51
         (494 letters)



>FitnessBrowser__Koxy:BWI76_RS15105
          Length = 504

 Score =  232 bits (591), Expect = 3e-65
 Identities = 148/459 (32%), Positives = 235/459 (51%), Gaps = 13/459 (2%)

Query: 3   MGIRTGAQYISGLKSRKPEIWLSGRRVINVCEEPVFKQPIREIARLYDMQHDPEYQDKIT 62
           + + TG  +++GL   + EIW  G +V NV   P F+     IA+LYD  HD +YQ  +T
Sbjct: 6   VSLPTGNDFLAGLNDGR-EIWAYGEKVDNVITHPAFRNSALSIAKLYDALHDEKYQAILT 64

Query: 63  HIC-TETGERVSNAFLVPKSREDLLARRALFEVWARATFGLMGRTPDFLNVVLTSLYSNA 121
             C T +G      F VP S +DL+  R     WAR ++G +GR+PDF    LT+L +N 
Sbjct: 65  TPCDTGSGGVTHPFFRVPHSVDDLIRDRDAIAQWARLSYGWLGRSPDFKASFLTTLGANP 124

Query: 122 SFLEKYNPQWAENIRAYYRYVRDNDLFLTHAIINPQNDRSKPSHEQQDTFTHLGVVRETP 181
              E Y  ++A+N R +Y+  ++  L+  HAIINP  DR+ P  + +D   H  V +E  
Sbjct: 125 ---EAYG-EYADNARHWYKRSQEELLYWNHAIINPPIDRNLPPDQIEDICIH--VEKECD 178

Query: 182 EGLIVRGAKMLATLAPITDEVIIYTFPGYKPGDERYAVSFAIPIDTPGLRILCREPMQDG 241
           +G+IV GAK++AT + +T    I  + G       +A+   +P++ PGL+++CR      
Sbjct: 179 DGVIVSGAKVVATGSALTHYNFIAHY-GLPVKKREFALVCTLPMNAPGLKLVCRPSYSLA 237

Query: 242 TRPL---FDHPLASRFEEMDALLVFNDVLVPWDRVFIYNNVEAANLLYPKTGIAQQPAHQ 298
              +   FD+PL+SR++E D + + + V +PW+ +FIY +   A    P +G   +    
Sbjct: 238 AEKIGSPFDYPLSSRYDENDMIFILDKVKIPWENIFIYGDTAKAATFLPSSGFLHRSTFH 297

Query: 299 TGVRGLIKLQFATEVAIRLADSIGVDVYLNVQNDLGELLQSVEAIRALLHLAEHELEVLP 358
              R  +K+ F   + I+  ++ GV  +  +Q  +GE+L       A+            
Sbjct: 298 GVTRLAVKIDFICGLFIKGVEATGVADFRGIQTRVGEMLAWRNLFWAISDAMAKSPNPWH 357

Query: 359 SGEVMPGWVPLETIRGLLPKLYPRAVEVL-QIIGAGGLLMSPTGADFANPELAADMEKYY 417
           +G ++P        R  +   YPR  E++ Q +G+  + ++    DFA PEL   ++KY 
Sbjct: 358 NGALLPNLDYGLAYRWFMSLGYPRIREIIEQDLGSALIYINSHAKDFAAPELEPYLKKYM 417

Query: 418 AGRIGVGGEERVRLFKLAWDLCGEAFGQRLLQYERFYTG 456
            G  G+   ERV+L KL WD  G  F  R   YER YTG
Sbjct: 418 RGSNGMDAVERVKLMKLIWDSVGTEFASRHELYERNYTG 456


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: 559
Number of extensions: 31
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: 504
Length adjustment: 34
Effective length of query: 460
Effective length of database: 470
Effective search space:   216200
Effective search space used:   216200
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