Alignments for a candidate for putA in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Nocardioides daejeonensis MJ31

Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_110208571.1 DNK54_RS18915 L-glutamate gamma-semialdehyde dehydrogenase

Query= SwissProt::Q8CHT0
         (562 letters)



>NCBI__GCF_003194585.1:WP_110208571.1
          Length = 549

 Score =  464 bits (1193), Expect = e-135
 Identities = 251/534 (47%), Positives = 330/534 (61%), Gaps = 6/534 (1%)

Query: 33  NEPILAFSQGSPERDALQKALKDLKGQMEAIPCVVGDEEVWTSDIQYQL-SPFNHAHKVA 91
           NEP L+++ G+ ER  L   L    G +  +   +G E V     + Q+  P  H   V 
Sbjct: 12  NEPNLSYAPGTAERAELAAELAAQVGTVRQLDAHIGGERVAGRGEEIQVVQPHAHQQVVG 71

Query: 92  KFCYADKALLNRAIDAALAARKEWDLKPMADRAQVFLKAADMLSGPRRAEVLAKTMVGQG 151
               +       AI AA  A   W      DRA + L+AA++L+GP R  + A T++GQ 
Sbjct: 72  VLRNSTADDTRAAIAAAREAAPGWRGLSYDDRAAILLRAAELLAGPWRQRLNAATVLGQS 131

Query: 152 KTVIQAEIDAAAELIDFFRFNAKFAVELEGEQPISVPPST-NHTVYRGLEGFVAAISPFN 210
           K+  QAEIDAA ELIDF+RFN  F  ++  EQPI   P   N T +R LEGFV AI+PFN
Sbjct: 132 KSPFQAEIDAACELIDFWRFNVHFGRQILAEQPIRNAPGVWNRTDHRPLEGFVYAITPFN 191

Query: 211 FTAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTFGD 270
           FTAI GNL  APALMGN VLWKPS T  LA+     +L EAG+PP +I  +P DG    +
Sbjct: 192 FTAIAGNLPTAPALMGNTVLWKPSPTQQLAASLTMELLEEAGMPPGVINMLPGDGLAVSE 251

Query: 271 TVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADVDS 330
              +   L GI+FTGS PTF+HLWR V +NL  +R++PRL GE GGK+F   H SAD   
Sbjct: 252 VALADPGLAGIHFTGSTPTFQHLWRTVGENLSSYRSYPRLVGETGGKDFVIAHPSADPAV 311

Query: 331 VVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAV 390
           + +  +R AFEY GQKCSA SR YVP+SLW ++   L+ E   + +GDP  DF  F  AV
Sbjct: 312 LRTALIRGAFEYAGQKCSAASRAYVPRSLWARMGDDLIAETDALPIGDPT-DFANFTGAV 370

Query: 391 IDAKAFARIKKWLEHARSSPSLSILAGGQCNESVGYYVEPCIIESKDPQEPIMKEEIFGP 450
           ID +AFA+ K  +E A S+  L ++AGG  ++SVG++V P I+ ++DP + + + E FGP
Sbjct: 371 IDGRAFAKHKAAIERASSTAGLHVVAGGTVDDSVGWFVRPTIVVAEDPADEMFRTEYFGP 430

Query: 451 VLTVYVYPDDK---YRETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYIND 507
           +L ++VY D +   + E ++  +S   Y LTGAV A D+  +  A+  LR AAGNFY+ND
Sbjct: 431 ILALHVYDDTRPGAFEEIVRQAESMAPYALTGAVLATDRRAIDWASEELRFAAGNFYVND 490

Query: 508 KSTGSVVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWRYSYM 561
           K TG+VVGQQPFGGARASGTNDK G    +LRWTS + IKET  P  D RY +M
Sbjct: 491 KPTGAVVGQQPFGGARASGTNDKAGSMLNLLRWTSARSIKETLVPPIDHRYPHM 544


Lambda     K      H
   0.319    0.135    0.411 

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: 853
Number of extensions: 33
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: 562
Length of database: 549
Length adjustment: 36
Effective length of query: 526
Effective length of database: 513
Effective search space:   269838
Effective search space used:   269838
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: 53 (25.0 bits)

Align candidate WP_110208571.1 DNK54_RS18915 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01236 (pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.1892993.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-236  769.5   0.0   9.9e-236  769.3   0.0    1.0  1  NCBI__GCF_003194585.1:WP_110208571.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003194585.1:WP_110208571.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  769.3   0.0  9.9e-236  9.9e-236       2     532 ..      12     544 ..      11     545 .. 0.99

  Alignments for each domain:
  == domain 1  score: 769.3 bits;  conditional E-value: 9.9e-236
                             TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                           neP  +++pg+ er  l +el+   ++v+++   igg++v   +e i+vv+P+ hq+++++l n+t +d ++a
  NCBI__GCF_003194585.1:WP_110208571.1  12 NEPNLSYAPGTAERAELAAELAAQVGTVRQLDAHIGGERVAGRGEEIQVVQPHAHQQVVGVLRNSTADDTRAA 84 
                                           9************************************************************************ PP

                             TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147
                                           + aa +a   W  l ++draai+l+aa+ll+g++r+ ++aat+lgqsk+++qaeida++elidf+rfnv++ r
  NCBI__GCF_003194585.1:WP_110208571.1  85 IAAAREAAPGWRGLSYDDRAAILLRAAELLAGPWRQRLNAATVLGQSKSPFQAEIDAACELIDFWRFNVHFGR 157
                                           ************************************************************************* PP

                             TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220
                                           ++l+ qP  +apg++n++++rpleGfv+ai+Pfnftaia+nl++aPalmGn+v+WkPs t+ l++ l+m++le
  NCBI__GCF_003194585.1:WP_110208571.1 158 QILAEQPIRNAPGVWNRTDHRPLEGFVYAITPFNFTAIAGNLPTAPALMGNTVLWKPSPTQQLAASLTMELLE 230
                                           ************************************************************************* PP

                             TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293
                                           eaG+Ppgvin++p+dg +vs+v+lad+ la++hftGst++f++lw++v +nl+ yr++Pr+vGetGGkdfv++
  NCBI__GCF_003194585.1:WP_110208571.1 231 EAGMPPGVINMLPGDGLAVSEVALADPGLAGIHFTGSTPTFQHLWRTVGENLSSYRSYPRLVGETGGKDFVIA 303
                                           ************************************************************************* PP

                             TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksf 366
                                           hpsad  ++++a+irgafey Gqkcsaasr+yvp+slw ++ ++l+ae++ + +gd++d+ +f+gavid ++f
  NCBI__GCF_003194585.1:WP_110208571.1 304 HPSADPAVLRTALIRGAFEYAGQKCSAASRAYVPRSLWARMGDDLIAETDALPIGDPTDFANFTGAVIDGRAF 376
                                           ************************************************************************* PP

                             TIGR01236 367 akivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvyddd...kykei 436
                                           ak + +ie+a + +  l+++aGG +dds G+fv+Pt+v ++dP ++++++e+fGP+l+++vydd+    ++ei
  NCBI__GCF_003194585.1:WP_110208571.1 377 AKHKAAIERASSTA-GLHVVAGGTVDDSVGWFVRPTIVVAEDPADEMFRTEYFGPILALHVYDDTrpgAFEEI 448
                                           **********9966.**************************************************7778**** PP

                             TIGR01236 437 levvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkill 509
                                           ++  +s + yaltGav+a dr+ai  a+++lrfaaGnfy+ndk+tGavvgqqpfGGar+sGtndkaG++ +ll
  NCBI__GCF_003194585.1:WP_110208571.1 449 VRQAESMAPYALTGAVLATDRRAIDWASEELRFAAGNFYVNDKPTGAVVGQQPFGGARASGTNDKAGSMLNLL 521
                                           ************************************************************************* PP

                             TIGR01236 510 rfvsarsiketfkeltdfkypym 532
                                           r++sarsiket++++ d++yp+m
  NCBI__GCF_003194585.1:WP_110208571.1 522 RWTSARSIKETLVPPIDHRYPHM 544
                                           **********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (549 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 33.79
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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