Aligments for a candidate for hpaH in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments 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:

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, or view the source code.

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