Alignments for a candidate for gloB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Cupriavidus basilensis 4G11

Align hydroxyacylglutathione hydrolase (EC 3.1.2.6) (characterized)
to candidate RR42_RS13570 RR42_RS13570 hydroxyacylglutathione hydrolase

Query= BRENDA::Q8ZRM2
         (251 letters)



>FitnessBrowser__Cup4G11:RR42_RS13570
          Length = 267

 Score =  183 bits (464), Expect = 4e-51
 Identities = 109/268 (40%), Positives = 148/268 (55%), Gaps = 20/268 (7%)

Query: 1   MNLNSIPAFQDNYIWVLTNDEGRCV-IVDPGEAAPVLKAIAEHKWMPEAIFLTHHHHDHV 59
           + +  IPAFQDNYIW +   +G C  +VDPGE+APV   +A       AI +THHH DH 
Sbjct: 2   LKVEPIPAFQDNYIWAI--HDGHCAAVVDPGESAPVEAFLAREGLTLGAIVITHHHGDHQ 59

Query: 60  GGVKELLQHFPQ------MTVYGPAETQDKGATHLVGDGDTIRVLGEKFTL--FATPGHT 111
           GGV  LL   P       + V GPA  +    T  V +GDT+ V      L     PGHT
Sbjct: 60  GGVAGLLAVHPTAPDGAPLPVIGPAGERIGARTVAVREGDTVNVAHPSLQLKVLDVPGHT 119

Query: 112 LGHVCYFSR-----PYLFCGDTLFSGGCGRLFEGTPSQMYQSLMKINSLPDDTLICCAHE 166
            GHV Y +      P +FCGDTLF+ GCGRLFEG+P+QM  SL K+ +LP  T + CAHE
Sbjct: 120 AGHVAYVADLPGAGPSVFCGDTLFASGCGRLFEGSPAQMLSSLDKLAALPGATRVYCAHE 179

Query: 167 YTLANIKFALSILPHDSFINEYYRKVKELRVKKQMTLPVILKNERKINLFLRTEDIDLIN 226
           YT +N++FA ++ PH++ +  +  +V  LR     T+P  +  ER++N FLR+  +  + 
Sbjct: 180 YTRSNVRFARAVEPHNAELAAWEARVDALRAVGAPTVPTTIGQEREVNPFLRSR-VPAVR 238

Query: 227 E---INKETILQQPEARFAWLRSKKDTF 251
           E    +   +     A F  LR  KD F
Sbjct: 239 EAVAAHAGGVAGNDAAAFGALRGWKDDF 266


Lambda     K      H
   0.323    0.140    0.436 

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: 209
Number of extensions: 9
Number of successful extensions: 5
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: 267
Length adjustment: 24
Effective length of query: 227
Effective length of database: 243
Effective search space:    55161
Effective search space used:    55161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate RR42_RS13570 RR42_RS13570 (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.29458.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.7e-95  305.1   0.0    1.9e-95  304.9   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS13570  RR42_RS13570 hydroxyacylglutathi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS13570  RR42_RS13570 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.9   0.0   1.9e-95   1.9e-95       2     248 .]       5     266 ..       4     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 304.9 bits;  conditional E-value: 1.9e-95
                                 TIGR03413   2 iaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp.. 68 
                                               ++ipa++dNyiw+++d +  a+vvDpge++pv ++l+++gl+l ai++THhH DH ggva ll+ +p  
  lcl|FitnessBrowser__Cup4G11:RR42_RS13570   5 EPIPAFQDNYIWAIHDGH-CAAVVDPGESAPVEAFLAREGLTLGAIVITHHHGDHQGGVAGLLAVHPta 72 
                                               78****************.99*****************************************9876532 PP

                                 TIGR03413  69 .....vkvvgpaeeripgltkevkegdevel..lelevevlevpGHtlgHiayyleee...kvlFcgDt 127
                                                    ++v+gpa eri + t++v+egd+v++   +l+++vl+vpGHt+gH+ay+++     + +FcgDt
  lcl|FitnessBrowser__Cup4G11:RR42_RS13570  73 pdgapLPVIGPAGERIGARTVAVREGDTVNVahPSLQLKVLDVPGHTAGHVAYVADLPgagPSVFCGDT 141
                                               2333478***********************955578999***************99656779******* PP

                                 TIGR03413 128 LfsaGCGrlfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealra 196
                                               Lf+ GCGrlfeg+++qml+sl+klaaLp +t+vycaHEYt sN+rFa+avep+n++l+++ ++v+alra
  lcl|FitnessBrowser__Cup4G11:RR42_RS13570 142 LFASGCGRLFEGSPAQMLSSLDKLAALPGATRVYCAHEYTRSNVRFARAVEPHNAELAAWEARVDALRA 210
                                               ********************************************************************* PP

                                 TIGR03413 197 kgkptlPstlaeekatNpFLraeeaevkaalee....ekaeevevfaelRekkdkf 248
                                                g pt+P+t+++e+++NpFLr + ++v++a+++     + +++++f +lR +kd+f
  lcl|FitnessBrowser__Cup4G11:RR42_RS13570 211 VGAPTVPTTIGQEREVNPFLRSRVPAVREAVAAhaggVAGNDAAAFGALRGWKDDF 266
                                               *****************************9999888888999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (267 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 5.96
//
[ok]

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
the source code
instructions for running GapMind on your computer

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