GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutH in Pseudomonas fluorescens FW300-N2C3

Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate AO356_09175 AO356_09175 histidine ammonia-lyase

Query= curated2:A9WHT8
         (523 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09175
          Length = 514

 Score =  267 bits (682), Expect = 8e-76
 Identities = 194/519 (37%), Positives = 269/519 (51%), Gaps = 25/519 (4%)

Query: 1   MQIREVILDGES-LTIEQVLAVAYGQPGTPVVRLAPIARQRVERAAQAVQDLLARGVVAY 59
           M   E +  GE  L IE VLA+A  Q  T + +  P  RQR+ + AQ +  LL +  V Y
Sbjct: 3   MPTLEPVTFGERPLRIEDVLALANRQAPTQL-QDDPAFRQRIAKGAQFLDSLLDKEGVIY 61

Query: 60  GITTGFGAFKDRVIAPDQVERLQYNILVSHAVGVGPVFDIPTTRAIMLIRANTLARGHSG 119
           G+TTG+G      +    VE L  ++   H  G+G + D   TRA++  R  +L  G SG
Sbjct: 62  GVTTGYGDSCVVAVPLHHVEALPRHLYTFHGCGLGKLLDAQATRAVLAARLQSLCHGVSG 121

Query: 120 VRLQTVERLLDMLNQGIHPRIPCKGSLGASGDLAPLAHMALPLIGLGEVEWQGEVLPAAT 179
           VR++ +ERL   L   I P IP +GS+GASGDL PL+++A  L G  EV ++GE   AA 
Sbjct: 122 VRVELLERLQAFLEHDILPLIPEEGSVGASGDLTPLSYVAATLSGEREVMFRGERRLAAD 181

Query: 180 ALERLGWQPLHLAAKEGLALTNGTAVMCALGVIETARAETLSATADIAGCLSLEALYGTP 239
               LGW PL L  KE LAL NGTAVM  L  +  ARA+ L   A     L++ AL G P
Sbjct: 182 VHRELGWTPLVLRPKEALALMNGTAVMTGLACLAFARADYLLQLATRITALNVVALQGNP 241

Query: 240 AAFDARLHALRPFPRQIECAAHLRRLLAGSTFVRNNDPRH-VQDAYTLRCIPQVHGAVRD 298
             FD RL A +P P Q++ AA LR+ LA         P H +QD Y+LRC P V G + D
Sbjct: 242 EHFDERLFAAKPHPGQMQVAAWLRKDLA---IDAPTAPLHRLQDRYSLRCAPHVLGVLAD 298

Query: 299 AIAYARWVFAIELNAVTDNPLLFVDDDGNVEVISGGNFHGEPLAIALDYLGLAVAELGNI 358
           ++ + R     ELN+  DNP++  + +    V+ GG+F+G  +A A+D L   VA + ++
Sbjct: 299 SLGWLRSFIETELNSANDNPIIDAEAE---RVLHGGHFYGGHIAFAMDSLKNLVANVADL 355

Query: 359 AERRLMRLTDEASNTHVLPAFLTRAGG----LNSGFMIVQYTAAALATENKVLAHPASVD 414
            +R+L  L DE  N H LP+ L+ A      LN GF  VQ   +A   E      PASV 
Sbjct: 356 LDRQLALLVDERYN-HGLPSNLSGASAERAMLNHGFKAVQIGTSAWTAEALKNTMPASVF 414

Query: 415 SIPTSANVEDHVSMGVTAGLKLRSIIDNVSQILALELFAAAQGIDFRRQELGSQARLGRG 474
           S  T  + +D VSMG  A      +++   Q+ A  L AA QG+  R     S+A   R 
Sbjct: 415 SRSTECHNQDKVSMGTIAARDAIRVLELTEQVAAATLLAANQGVWLR-----SRAEDARP 469

Query: 475 TGPV-----YELIRQYVPFIAEDTLLHPYITIISELVAQ 508
             P       +L   + P I ED  L   + +  + +A+
Sbjct: 470 LPPALAAMHQQLAEDFAPVI-EDRALEGELRLCLQRIAE 507


Lambda     K      H
   0.322    0.137    0.396 

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: 602
Number of extensions: 25
Number of successful extensions: 4
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: 523
Length of database: 514
Length adjustment: 35
Effective length of query: 488
Effective length of database: 479
Effective search space:   233752
Effective search space used:   233752
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