GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Halomonas xinjiangensis TRM 0175

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate WP_043526145.1 JH15_RS00990 hydroxyacylglutathione hydrolase

Query= CharProtDB::CH_024825
         (251 letters)



>NCBI__GCF_000759345.1:WP_043526145.1
          Length = 255

 Score =  213 bits (541), Expect = 4e-60
 Identities = 111/250 (44%), Positives = 151/250 (60%), Gaps = 5/250 (2%)

Query: 6   IPAFDDNYIWVLN-DEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVGGVKE 64
           IPA  DNYIW+L  D +    +VDPGDA PV+  +         I +THHHHDH GG++ 
Sbjct: 7   IPALSDNYIWLLRQDTSNEVAVVDPGDARPVIELLEREGLTLGTILITHHHHDHTGGLEA 66

Query: 65  LVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFSK---P 121
           L+ ++   V+ GPQ     G  + + +G+   VLG  F V+  PGHTL HI +F+    P
Sbjct: 67  LIRQYRPRVI-GPQNPDIVGIDERLAEGDECHVLGRRFEVLEMPGHTLDHIAFFAAGIPP 125

Query: 122 YLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSILPH 181
            L  GD LFSGGCGRLFEGT  QM+ SL KL+ALPD+TL+  AHEYTL+N++FA +  P 
Sbjct: 126 LLLAGDALFSGGCGRLFEGTPEQMHASLAKLAALPDETLIFAAHEYTLANLRFAKAADPD 185

Query: 182 DLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLLQQPEERF 241
           + +I  Y  + + +R +++ TLP  L  ERQ+N FLRTE   + N  + +         F
Sbjct: 186 NPAIGAYLEECQRVRDQDKPTLPTQLARERQVNPFLRTEQPGVRNAASAQGDTTTSLATF 245

Query: 242 AWLRSKKDRF 251
             LR+ KDRF
Sbjct: 246 TTLRAWKDRF 255


Lambda     K      H
   0.321    0.138    0.425 

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: 219
Number of extensions: 13
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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: 46 (22.3 bits)

Align candidate WP_043526145.1 JH15_RS00990 (hydroxyacylglutathione hydrolase)
to HMM TIGR03413 (gloB: hydroxyacylglutathione hydrolase (EC 3.1.2.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03413.hmm
# target sequence database:        /tmp/gapView.3744514.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03413  [M=248]
Accession:   TIGR03413
Description: GSH_gloB: hydroxyacylglutathione hydrolase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-102  326.9   0.0   4.2e-102  326.8   0.0    1.0  1  NCBI__GCF_000759345.1:WP_043526145.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043526145.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.8   0.0  4.2e-102  4.2e-102       2     248 .]       5     255 .]       4     255 .] 0.98

  Alignments for each domain:
  == domain 1  score: 326.8 bits;  conditional E-value: 4.2e-102
                             TIGR03413   2 iaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfpvkvvg 73 
                                            +ipalsdNyiwll++++s e++vvDpg+a+pv+e le++gl+l +il+THhH+DH+gg ++l+++++ +v+g
  NCBI__GCF_000759345.1:WP_043526145.1   5 LPIPALSDNYIWLLRQDTSnEVAVVDPGDARPVIELLEREGLTLGTILITHHHHDHTGGLEALIRQYRPRVIG 77 
                                           689************99999***************************************************** PP

                             TIGR03413  74 paeeripgltkevkegdevellelevevlevpGHtlgHiayyleee.kvlFcgDtLfsaGCGrlfegtaeqml 145
                                           p++ +i g++++++egde+++l++++evle+pGHtl+Hia++++   ++l +gD+Lfs GCGrlfegt+eqm+
  NCBI__GCF_000759345.1:WP_043526145.1  78 PQNPDIVGIDERLAEGDECHVLGRRFEVLEMPGHTLDHIAFFAAGIpPLLLAGDALFSGGCGRLFEGTPEQMH 150
                                           ******************************************9977799************************ PP

                             TIGR03413 146 eslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLra 218
                                           +sl klaaLp+et++++aHEYtl+NlrFa+a++p+n+a+ ++l+e+++ r+++kptlP++la+e+++NpFLr+
  NCBI__GCF_000759345.1:WP_043526145.1 151 ASLAKLAALPDETLIFAAHEYTLANLRFAKAADPDNPAIGAYLEECQRVRDQDKPTLPTQLARERQVNPFLRT 223
                                           ************************************************************************* PP

                             TIGR03413 219 eeaevkaalee..ekaeevevfaelRekkdkf 248
                                           e++ v++a+++  ++++++++f++lR++kd+f
  NCBI__GCF_000759345.1:WP_043526145.1 224 EQPGVRNAASAqgDTTTSLATFTTLRAWKDRF 255
                                           ******99999777889999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (255 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 14.32
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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