GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proC in Marinobacter adhaerens HP15

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate GFF288 HP15_287 pyrroline-5-carboxylate reductase

Query= SwissProt::P22008
         (273 letters)



>FitnessBrowser__Marino:GFF288
          Length = 277

 Score =  234 bits (598), Expect = 1e-66
 Identities = 123/271 (45%), Positives = 177/271 (65%), Gaps = 1/271 (0%)

Query: 2   STPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAV 61
           ++P I+FIGAGNMA+++IGG+   G  A  I  S P       I   F + V   N    
Sbjct: 3   TSPTISFIGAGNMASAIIGGMLDNGYKAGNIWVSAPDDAHLQTIRKRFGVSVTTDNRYCA 62

Query: 62  ADADVVVLSVKPQAMKAVCQALAPALKPEQ-LIVSIAAGIPCASLEAWLGQPRPVVRCMP 120
             AD+VVL+VKPQ M  VC+ +AP ++  + L+VSIAAG+   +L+ WLG   P+VR MP
Sbjct: 63  QQADMVVLAVKPQVMADVCRDIAPVVQNTRPLMVSIAAGLTADTLDGWLGGGLPMVRVMP 122

Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180
           NTP+L+ +GA+GL+AN +V   Q +    +  ++G ALW++DE  + AVTA+SGSGPAYF
Sbjct: 123 NTPSLVGKGAAGLFANKEVKDKQKKMVESVFESIGSALWVEDENLLHAVTALSGSGPAYF 182

Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240
           FL+++A+ +A  + G++  TA  L +QT  GAA+MA  SE +P +L+R V SP GTTE A
Sbjct: 183 FLMLEALEEAATEAGIAAGTARELAIQTMAGAAEMAGRSEHDPGQLKRNVMSPGGTTEQA 242

Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQL 271
           I +F+  G   LV +A  AA +RS E+A++L
Sbjct: 243 INTFEEGGMRDLVAKAYKAAFKRSEEMAKEL 273


Lambda     K      H
   0.315    0.127    0.348 

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: 190
Number of extensions: 6
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: 273
Length of database: 277
Length adjustment: 25
Effective length of query: 248
Effective length of database: 252
Effective search space:    62496
Effective search space used:    62496
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 GFF288 HP15_287 (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.4063.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.1e-88  283.2   1.4    1.3e-88  283.1   1.4    1.0  1  lcl|FitnessBrowser__Marino:GFF288  HP15_287 pyrroline-5-carboxylate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF288  HP15_287 pyrroline-5-carboxylate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.1   1.4   1.3e-88   1.3e-88       1     263 []       7     269 ..       7     269 .. 0.99

  Alignments for each domain:
  == domain 1  score: 283.1 bits;  conditional E-value: 1.3e-88
                          TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevl 76 
                                        i++iGaGnm++a++ g+l +g k + +i+v ++ +++l+   k++gv+vt+d++ ++++ad+v+lavKPq++ +v+
  lcl|FitnessBrowser__Marino:GFF288   7 ISFIGAGNMASAIIGGMLDNGYK-AGNIWVSAPDDAHLQTIRKRFGVSVTTDNRYCAQQADMVVLAVKPQVMADVC 81 
                                        79*****************9877.8*************************************************** PP

                          TIGR00112  77 aelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavG 152
                                        ++++   ++   l++Si+AG+t+++l  +l++  ++vRvmPNt++ vg+g+++++a++ev+++qk+ ve++++++G
  lcl|FitnessBrowser__Marino:GFF288  82 RDIAPVVQNTRPLMVSIAAGLTADTLDGWLGGGLPMVRVMPNTPSLVGKGAAGLFANKEVKDKQKKMVESVFESIG 157
                                        *****99999****************************************************************** PP

                          TIGR00112 153 kvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVt 227
                                        ++++ve e+ll+avtalsGSgPA++fl++eal++a++++G+ + +a+ela qt++Gaa++  +s+++p +Lk +V+
  lcl|FitnessBrowser__Marino:GFF288 158 SALWVEdENLLHAVTALSGSGPAYFFLMLEALEEAATEAGIAAGTARELAIQTMAGAAEMAGRSEHDPGQLKRNVM 233
                                        ****************************************************************9*********** PP

                          TIGR00112 228 sPgGtTiaglavLeekgvrsavieaveaavkrseeL 263
                                        sPgGtT ++++++ee+g+r+ v++a +aa krsee+
  lcl|FitnessBrowser__Marino:GFF288 234 SPGGTTEQAINTFEEGGMRDLVAKAYKAAFKRSEEM 269
                                        *********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (277 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.32
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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