GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proC in Lentibacillus jeotgali Grbi

Align Pyrroline-5-carboxylate reductase 2; P5C reductase 2; P5CR 2; PCA reductase 2; EC 1.5.1.2 (characterized)
to candidate WP_010531255.1 ON01_RS11815 pyrroline-5-carboxylate reductase

Query= SwissProt::P54552
         (278 letters)



>NCBI__GCF_000224785.1:WP_010531255.1
          Length = 271

 Score =  223 bits (569), Expect = 3e-63
 Identities = 119/265 (44%), Positives = 171/265 (64%), Gaps = 1/265 (0%)

Query: 2   KKIGFVGAGSMAEAMINGILQSGITKPEHIYITNRSNDERLIELKETYSVRPCRDKNEFF 61
           +K+ F+GAGSMAE+++ GIL S     E I++TN+S+  RL  L++ Y V+   +  +  
Sbjct: 3   EKLAFIGAGSMAESILTGILNSEFFPKEKIFVTNKSDKNRLEFLEKQYEVQNTDNTQQTV 62

Query: 62  THTDIIILAFKPKDAAESIDSIRPYI-KDQLVISVLAGLTIETIQHYFGRKLAVIRVMPN 120
              DI+I+A KP D   ++ SIR Y+ K QL+ISV+AG++ +TI     +++ V+R MPN
Sbjct: 63  DGADIVIIAVKPYDVEAALTSIRNYLDKGQLLISVVAGISTDTISQLINKEVPVVRAMPN 122

Query: 121 TSAAIRKSATGFSVSTEASKNDIIAAKALLETIGDATLVEERHLDAVTAIAGSGPAYVYR 180
           TS+A  +SAT  +    A    +  A  L  TIG AT V E  +  VTAI+GSGPAY+Y 
Sbjct: 123 TSSAAGQSATAVTRGKFAMAEHLQTALDLFNTIGTATEVAETDMHTVTAISGSGPAYIYY 182

Query: 181 YIEAMEKAAQKVGLDKETAKALILQTMAGATDMLLQSGKQPEKLRKEITSPGGTTEAGLR 240
            +EAME AA + GLD +TA  LI QT+ GA +ML  SG  P +LR+ ITSPGGTT+AGL 
Sbjct: 183 LVEAMELAAVRAGLDHDTAHDLITQTIVGAGEMLTTSGLDPSRLRENITSPGGTTQAGLE 242

Query: 241 ALQDSRFEEAIIHCIEETAKRSAEI 265
           +L +  F+E ++ C+E   +RS E+
Sbjct: 243 SLAEHNFQETVMSCVESARERSIEL 267


Lambda     K      H
   0.316    0.131    0.353 

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: 200
Number of extensions: 8
Number of successful extensions: 2
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: 278
Length of database: 271
Length adjustment: 25
Effective length of query: 253
Effective length of database: 246
Effective search space:    62238
Effective search space used:    62238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate WP_010531255.1 ON01_RS11815 (pyrroline-5-carboxylate reductase)
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))

# 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.aa/TIGR00112.hmm
# target sequence database:        /tmp/gapView.2124758.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00112  [M=263]
Accession:   TIGR00112
Description: proC: pyrroline-5-carboxylate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-89  286.2   3.0    1.5e-89  286.1   3.0    1.0  1  NCBI__GCF_000224785.1:WP_010531255.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010531255.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.1   3.0   1.5e-89   1.5e-89       1     263 []       5     267 ..       5     267 .. 0.98

  Alignments for each domain:
  == domain 1  score: 286.1 bits;  conditional E-value: 1.5e-89
                             TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKPqdl 72 
                                           +a+iGaG+m+e++l+g+l+++   k++i v+++s +++l+ l k+++v+ t + ++ v+ ad+v++avKP+d+
  NCBI__GCF_000224785.1:WP_010531255.1   5 LAFIGAGSMAESILTGILNSEFFPKEKIFVTNKSdKNRLEFLEKQYEVQNTDNTQQTVDGADIVIIAVKPYDV 77 
                                           69********************************88889999999**************************** PP

                             TIGR00112  73 eevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelve 145
                                           e++l+++++    k++lliS++AG+++++++ql+++e +vvR+mPNt+++ g+++ta++ ++++ +e+ +++ 
  NCBI__GCF_000224785.1:WP_010531255.1  78 EAALTSIRN-YLDKGQLLISVVAGISTDTISQLINKEVPVVRAMPNTSSAAGQSATAVTRGKFAMAEHLQTAL 149
                                           ******999.5559*********************************************************** PP

                             TIGR00112 146 ellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgeh 218
                                           +l++++G+++ev+e ++++vta+sGSgPA++++l+ea++ a+v++GL++++a +l++qt+ Ga+++l+ sg +
  NCBI__GCF_000224785.1:WP_010531255.1 150 DLFNTIGTATEVAETDMHTVTAISGSGPAYIYYLVEAMELAAVRAGLDHDTAHDLITQTIVGAGEMLTTSGLD 222
                                           ************************************************************************* PP

                             TIGR00112 219 palLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263
                                           p++L++++tsPgGtT+agl++L e++++++v+ +ve+a +rs eL
  NCBI__GCF_000224785.1:WP_010531255.1 223 PSRLRENITSPGGTTQAGLESLAEHNFQETVMSCVESARERSIEL 267
                                           *****************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (271 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: 17.98
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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