Alignments for a candidate for astD in Novosphingobium barchaimii LL02

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Novosphingobium barchaimii LL02

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_059151695.1 V474_RS11820 succinylglutamate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>NCBI__GCF_001046635.1:WP_059151695.1
          Length = 474

 Score =  456 bits (1172), Expect = e-132
 Identities = 230/453 (50%), Positives = 309/453 (68%), Gaps = 4/453 (0%)

Query: 21  NPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLESNKAELT 80
           +P +GE +W+G  A    V  A   AR AFP WA L  AER A  +R+ A LE+ K  + 
Sbjct: 8   DPATGETVWEGEIAGPQAVSAALLRARKAFPAWAALPVAERVAAAQRYKAALEARKDAIA 67

Query: 81  AIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPDGAASLRHRPHGVLAV 140
            IIARETGKP WE  TEV +MI K+ +SI A   R G+++S MP G A LRHRPHGV+AV
Sbjct: 68  QIIARETGKPMWETRTEVASMIGKVGLSITAQAERAGDRQSAMPFGQAVLRHRPHGVMAV 127

Query: 141 FGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRLWQQA-GLPPGVLNLVQG 199
            GP+NFPGHLPNGHIVPAL+AGNT++FKPSE+TP +G A+   W +A      V   +QG
Sbjct: 128 LGPFNFPGHLPNGHIVPALIAGNTVVFKPSEMTPATGAAMAECWAEALADHRHVFQCIQG 187

Query: 200 GRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEMGGNNPLIIDEVADID 259
            RETG+AL A   +DGLLFTGSA  G    R  + +P+ ILALE+GGNNPLI  + AD+D
Sbjct: 188 ARETGEALVA-GHIDGLLFTGSAGAGAHFRRIFADRPDVILALELGGNNPLIAWDSADVD 246

Query: 260 AAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDDEPQPFIG 319
            A  + +QS F+T GQRC+CARRL++   A G A +  +  ++ R+  G W++ P+P+IG
Sbjct: 247 EAASVVVQSGFITTGQRCSCARRLIVPDNAFGAALVDAVAGLADRIVIGAWNETPEPWIG 306

Query: 320 GLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGT-SLLTPGIIEMTGVAGVPDEEVFG 378
            LIS+ AAQ     + +L   G + +     ++  + + +TP I+++TG+  VPDEE+F 
Sbjct: 307 PLISDAAAQAAKARFAELVERGAKVIRPLNGVEGRSGAFVTPAILDVTGIF-VPDEEIFA 365

Query: 379 PLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKPLTGAAS 438
           P+L++ R   FD AI  ANNTRFGLS GL+S +   + ++L+E RAG+VN N+P TGAA 
Sbjct: 366 PVLQISRVPDFDAAIEAANNTRFGLSAGLISADDALWQRVLVEGRAGVVNRNRPTTGAAG 425

Query: 439 TAPFGGIGASGNHRPSAWYAADYCAWPMASLES 471
           + PFGG+G SGNHRPSA+YAADYCA+P+AS E+
Sbjct: 426 SMPFGGLGESGNHRPSAYYAADYCAYPVASFEA 458


Lambda     K      H
   0.318    0.134    0.412 

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: 774
Number of extensions: 41
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: 492
Length of database: 474
Length adjustment: 34
Effective length of query: 458
Effective length of database: 440
Effective search space:   201520
Effective search space used:   201520
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_059151695.1 V474_RS11820 (succinylglutamate-semialdehyde dehydrogenase)
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

# 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/TIGR03240.hmm
# target sequence database:        /tmp/gapView.3564520.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03240  [M=484]
Accession:   TIGR03240
Description: arg_catab_astD: succinylglutamate-semialdehyde 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-198  644.9   4.9   5.4e-198  644.5   4.9    1.0  1  NCBI__GCF_001046635.1:WP_059151695.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059151695.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.5   4.9  5.4e-198  5.4e-198      15     472 ..       4     461 ..       2     470 .. 0.98

  Alignments for each domain:
  == domain 1  score: 644.5 bits;  conditional E-value: 5.4e-198
                             TIGR03240  15 lesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviaketgk 87 
                                           l+s dp+t+e++w+g+ a  + v++a+  arkafpawa+l+++er+a  +r+++ le +k+++a++ia+etgk
  NCBI__GCF_001046635.1:WP_059151695.1   4 LQSFDPATGETVWEGEIAGPQAVSAALLRARKAFPAWAALPVAERVAAAQRYKAALEARKDAIAQIIARETGK 76 
                                           789********************************************************************** PP

                             TIGR03240  88 plweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhivpallaG 160
                                           p+we+rtevasm++kv +si a +er+G+++s+++ ++avlrhrphGv+av+Gp+nfpGhlpnGhivpal+aG
  NCBI__GCF_001046635.1:WP_059151695.1  77 PMWETRTEVASMIGKVGLSITAQAERAGDRQSAMPFGQAVLRHRPHGVMAVLGPFNFPGHLPNGHIVPALIAG 149
                                           ************************************************************************* PP

                             TIGR03240 161 ntvvfkpseltplvaeetvklwekaGlp.aGvlnlvqGaretGkalaaeedidGllftGssntGallhrqlag 232
                                           ntvvfkpse+tp ++ ++ ++w++a      v++ +qGaretG+al+a  +idGllftGs+ +Ga+++r +a+
  NCBI__GCF_001046635.1:WP_059151695.1 150 NTVVFKPSEMTPATGAAMAECWAEALADhRHVFQCIQGARETGEALVAG-HIDGLLFTGSAGAGAHFRRIFAD 221
                                           ************************98762579***************98.9********************** PP

                             TIGR03240 233 rpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltv 305
                                           rp++ilalelGGnnpl+ ++ +d+d a+  +vqs fi++Gqrc+carrl+v+d+a G+al++++  +a+r+++
  NCBI__GCF_001046635.1:WP_059151695.1 222 RPDVILALELGGNNPLIAWDSADVDEAASVVVQSGFITTGQRCSCARRLIVPDNAFGAALVDAVAGLADRIVI 294
                                           ************************************************************************* PP

                             TIGR03240 306 gkydaepqpflGavisekaakellaaqekllalggksllelkqlee.eaalltpgiidvtevaevpdeeyfgp 377
                                           g++++ p+p++G++is+ aa++  a  ++l++ g+k +  l+ +e  + a++tp+i+dvt++  vpdee f+p
  NCBI__GCF_001046635.1:WP_059151695.1 295 GAWNETPEPWIGPLISDAAAQAAKARFAELVERGAKVIRPLNGVEGrSGAFVTPAILDVTGI-FVPDEEIFAP 366
                                           *********************999999*****************984568***********9.89******** PP

                             TIGR03240 378 llkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhr 450
                                           +l++ r+ dfd+a+++anntrfGl+aGl+s d++l++++l e raG+vn n+p+tGa++++pfGG+G sGnhr
  NCBI__GCF_001046635.1:WP_059151695.1 367 VLQISRVPDFDAAIEAANNTRFGLSAGLISADDALWQRVLVEGRAGVVNRNRPTTGAAGSMPFGGLGESGNHR 439
                                           ************************************************************************* PP

                             TIGR03240 451 psayyaadycaypvasleadsl 472
                                           psayyaadycaypvas+ea   
  NCBI__GCF_001046635.1:WP_059151695.1 440 PSAYYAADYCAYPVASFEATDA 461
                                           ******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (474 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: 25.88
//
[ok]

This GapMind analysis is from Sep 24 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 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