GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proC in Shewanella oneidensis MR-1

Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate 202462 SO3354 pyrroline-5-carboxylate reductase (NCBI ptt file)

Query= reanno::PV4:5208627
         (272 letters)



>FitnessBrowser__MR1:202462
          Length = 272

 Score =  362 bits (928), Expect = e-105
 Identities = 176/272 (64%), Positives = 220/272 (80%)

Query: 1   MTQKKICFIGAGNMTRSITSGLVKGGYAPELIHATNPSEGKLIALKQDLGIRVSHDNLQA 60
           M+Q+KICFIGAGNMTRSI SGL++ GY    + ATNPS+GKL AL  D G+RVS DN+ A
Sbjct: 1   MSQQKICFIGAGNMTRSIISGLIRSGYPASQVQATNPSQGKLDALATDFGVRVSQDNVSA 60

Query: 61  ADEADVIVLAVKPQLMQQVCEAMSGLNLKDKLIVTIAAGVTAERYHAFFKQPIQLIRTMP 120
           A +ADVI+L+VKPQLM+QVC+A+ G+++ +KL++TIAAG+ A RY  +  QPI LIRTMP
Sbjct: 61  AQDADVIILSVKPQLMEQVCQALQGIDMSNKLLITIAAGIKASRYSEYLAQPITLIRTMP 120

Query: 121 NTPTQIGLGMTGLYAEQGVSAQDRELCEQLMQTGGETVWVEKEEDLNQVIALAGSSPAYF 180
           NTP QIG+GMTGLYA Q +S   + + E+LM +GGE VWV +E D+NQVIALAGSSPAYF
Sbjct: 121 NTPMQIGVGMTGLYAPQSLSDAQKAIAERLMSSGGEIVWVNEESDINQVIALAGSSPAYF 180

Query: 181 FLMMEAMIDSAKQDGVDEQTAREMVQQAALGAAAMVKQNPQLSPAQLRENVTSKGGTTAQ 240
           FL+ME+MID+ KQ G+DE  AR +VQQAALGAA M KQNP+L+   LRENVTSKGGTTAQ
Sbjct: 181 FLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPELTLGNLRENVTSKGGTTAQ 240

Query: 241 ALAAFERAGLREIVRTAMHDCMDRAQEMAKQF 272
           A+A FE A LR +V+ AM +C++RA+EMAK F
Sbjct: 241 AIATFEAADLRGVVKKAMENCINRAEEMAKTF 272


Lambda     K      H
   0.317    0.130    0.361 

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: 258
Number of extensions: 3
Number of successful extensions: 1
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: 272
Length of database: 272
Length adjustment: 25
Effective length of query: 247
Effective length of database: 247
Effective search space:    61009
Effective search space used:    61009
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate 202462 SO3354 (pyrroline-5-carboxylate reductase (NCBI ptt file))
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.17016.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.9e-78  249.7   6.7    2.2e-78  249.5   6.7    1.0  1  lcl|FitnessBrowser__MR1:202462  SO3354 pyrroline-5-carboxylate r


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202462  SO3354 pyrroline-5-carboxylate reductase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.5   6.7   2.2e-78   2.2e-78       1     263 []       6     268 ..       6     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 249.5 bits;  conditional E-value: 2.2e-78
                       TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlael 79 
                                     i +iGaGnm ++++sgl+++g + ++++  +++s+ kl+ala+++gv+v++d+++a+++adv++l+vKPq +e+v++ l
  lcl|FitnessBrowser__MR1:202462   6 ICFIGAGNMTRSIISGLIRSGYP-ASQVQATNPSQGKLDALATDFGVRVSQDNVSAAQDADVIILSVKPQLMEQVCQAL 83 
                                     68******************888.8****************************************************** PP

                       TIGR00112  80 kseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvveve 158
                                     ++  ++ +klli+i+AG+++++++++l++  +++R mPNt+ ++g g+t+++a +  s++qk+ +e+l+++ G++v+v+
  lcl|FitnessBrowser__MR1:202462  84 QG-IDMSNKLLITIAAGIKASRYSEYLAQPITLIRTMPNTPMQIGVGMTGLYAPQSLSDAQKAIAERLMSSGGEIVWVN 161
                                     **.66699********************99************************************************* PP

                       TIGR00112 159 .eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge.hpalLkdkVtsPgGtTia 235
                                      e+++++v al+GS+PA++fll+e+++dag ++G+++++a++l++q+  Gaa + +++ e +   L+++Vts+gGtT++
  lcl|FitnessBrowser__MR1:202462 162 eESDINQVIALAGSSPAYFFLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPElTLGNLRENVTSKGGTTAQ 240
                                     999******************************************************99999***************** PP

                       TIGR00112 236 glavLeekgvrsavieaveaavkrseeL 263
                                     ++a++e++++r+ v +a+e++++r+ee+
  lcl|FitnessBrowser__MR1:202462 241 AIATFEAADLRGVVKKAMENCINRAEEM 268
                                     *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (272 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: 9.51
//
[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