Alignments for a candidate for astD in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Paraburkholderia bryophila 376MFSha3.1

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate H281DRAFT_06481 H281DRAFT_06481 succinylglutamic semialdehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974
         (488 letters)



>FitnessBrowser__Burk376:H281DRAFT_06481
          Length = 487

 Score =  604 bits (1557), Expect = e-177
 Identities = 300/486 (61%), Positives = 370/486 (76%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M  L+I GEW AG G AF S NP T   +W G  A+A  V+ AV++AR+AF  W+  +L+
Sbjct: 1   MSELFIDGEWAAGTGPAFASRNPGTGATVWEGNSASADDVDRAVRSARRAFATWSASSLD 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ER +V+  FAA +    + LA  IG ETGKPLWEA TE  SM  K+ IS+QSY ERTGEK
Sbjct: 61  ERCAVVRRFAALVTERKEALAEAIGRETGKPLWEARTEAASMAAKVEISIQSYNERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
              + D TAVLRH+PHGVVAVFGPYNFPGHLPNGHIVPAL+AGN+V+FKPSEL P VA L
Sbjct: 121 RSAMADGTAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNAVVFKPSELAPGVAAL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TV+ W +AGLPAGVLNL+QG ++TGIALA +  IDGLFFTGSS TG  LH+QF GRP+ +
Sbjct: 181 TVQTWRDAGLPAGVLNLVQGEKDTGIALANHRQIDGLFFTGSSDTGALLHKQFGGRPEIV 240

Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300
           LALEMGGNNPLV+  VADLDAAV+  IQSAF+SAGQRCTCARR+ VP  A+G+  LARLV
Sbjct: 241 LALEMGGNNPLVIGPVADLDAAVHHTIQSAFLSAGQRCTCARRIFVPNDAFGERFLARLV 300

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
            V+S +SVG ++ +P PFMG+V+S  AA  L+ AQE LLA+GA ALL+M Q   +   +T
Sbjct: 301 EVTSRISVGEYNAEPQPFMGAVISARAASRLVAAQERLLADGAHALLKMEQRDPKLGFVT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           P ILDVSAV + PDEE FGPL Q+IRY  F+ A+ +ANDT +GL+AGLL+D E+ +  F 
Sbjct: 361 PAILDVSAVKNLPDEEHFGPLAQIIRYDSFDEALDKANDTEFGLSAGLLADDESLWTHFQ 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
              RAGIVNWN+   GA+S APFGG G SGNHR SAYYAADYCAYP+AS+E+  L +P++
Sbjct: 421 RTIRAGIVNWNRPTNGASSGAPFGGPGRSGNHRPSAYYAADYCAYPMASVESAQLQMPAS 480

Query: 481 LTPGVK 486
           ++PG++
Sbjct: 481 VSPGLQ 486


Lambda     K      H
   0.316    0.132    0.388 

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: 727
Number of extensions: 30
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: 488
Length of database: 487
Length adjustment: 34
Effective length of query: 454
Effective length of database: 453
Effective search space:   205662
Effective search space used:   205662
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: 52 (24.6 bits)

Align candidate H281DRAFT_06481 H281DRAFT_06481 (succinylglutamic 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.25068.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.6e-254  830.2   0.5     3e-254  830.1   0.5    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06481  H281DRAFT_06481 succinylglutamic


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06481  H281DRAFT_06481 succinylglutamic semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  830.1   0.5    3e-254    3e-254       1     484 []       4     487 .]       4     487 .] 1.00

  Alignments for each domain:
  == domain 1  score: 830.1 bits;  conditional E-value: 3e-254
                                    TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrf 66 
                                                  lfidG+w aG+G +++s++p t++++w+g++asa++v++av++ar+af++w++ sl+er+avv+rf
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481   4 LFIDGEWAAGTGPAFASRNPGTGATVWEGNSASADDVDRAVRSARRAFATWSASSLDERCAVVRRF 69 
                                                  59**************************************************************** PP

                                    TIGR03240  67 aelleeekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrp 132
                                                  a+l++e+ke+lae+i++etgkplwearte asm+akv+isi++y+ertGek+s++ad++avlrhrp
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481  70 AALVTERKEALAEAIGRETGKPLWEARTEAASMAAKVEISIQSYNERTGEKRSAMADGTAVLRHRP 135
                                                  ****************************************************************** PP

                                    TIGR03240 133 hGvlavfGpynfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGa 198
                                                  hGv+avfGpynfpGhlpnGhivpal+aGn+vvfkpsel+p va  tv+ w++aGlpaGvlnlvqG+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481 136 HGVVAVFGPYNFPGHLPNGHIVPALIAGNAVVFKPSELAPGVAALTVQTWRDAGLPAGVLNLVQGE 201
                                                  ****************************************************************** PP

                                    TIGR03240 199 retGkalaaeedidGllftGssntGallhrqlagrpekilalelGGnnplvveevkdidaavhliv 264
                                                  ++tG ala++++idGl+ftGss+tGallh+q++grpe++lale+GGnnplv+  v+d+daavh+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481 202 KDTGIALANHRQIDGLFFTGSSDTGALLHKQFGGRPEIVLALEMGGNNPLVIGPVADLDAAVHHTI 267
                                                  ****************************************************************** PP

                                    TIGR03240 265 qsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpflGavisekaakella 330
                                                  qsaf+saGqrctcarr++v+++a G+++l+rlvev++r+ vg+y+aepqpf+Gavis++aa++l+a
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481 268 QSAFLSAGQRCTCARRIFVPNDAFGERFLARLVEVTSRISVGEYNAEPQPFMGAVISARAASRLVA 333
                                                  ****************************************************************** PP

                                    TIGR03240 331 aqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlrykdfdealaeann 396
                                                  aqe+lla g+++ll+++q + + +++tp+i+dv++v+++pdee+fgpl +++ry++fdeal++an+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481 334 AQERLLADGAHALLKMEQRDPKLGFVTPAILDVSAVKNLPDEEHFGPLAQIIRYDSFDEALDKAND 399
                                                  ****************************************************************** PP

                                    TIGR03240 397 trfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycay 462
                                                  t+fGl+aGll+dd++l+ +f ++iraGivnwn+p++Gass apfGG G+sGnhrpsayyaadycay
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481 400 TEFGLSAGLLADDESLWTHFQRTIRAGIVNWNRPTNGASSGAPFGGPGRSGNHRPSAYYAADYCAY 465
                                                  ****************************************************************** PP

                                    TIGR03240 463 pvasleadslalpatlspGlkl 484
                                                  p+as+e+++l++pa++spGl++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06481 466 PMASVESAQLQMPASVSPGLQF 487
                                                  ********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (487 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.97
//
[ok]

This GapMind analysis is from Sep 17 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)
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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 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