Alignments for a candidate for astD in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Caulobacter crescentus NA1000

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_00618 CCNA_00618 succinylglutamic semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Caulo:CCNA_00618
          Length = 472

 Score =  490 bits (1261), Expect = e-143
 Identities = 254/471 (53%), Positives = 321/471 (68%), Gaps = 4/471 (0%)

Query: 15  ASR-VKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLE 73
           ASR + R+P +GE +      DA  ++ AC +ARAAF  WA    AER A+  RFA  + 
Sbjct: 3   ASRLISRDPYTGEAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVR 62

Query: 74  SNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPDGAASLRHR 133
           + + E+  +IARETGKP WEA TE  ++  K+AISI+A   R GE+   M D  A L HR
Sbjct: 63  ARREEIATLIARETGKPMWEALTEADSVAAKVAISIRAQDERAGERSEPMADATARLAHR 122

Query: 134 PHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRLWQQAGLPPGV 193
           PHGVLAV GP+NFP HL NGHIVPALLAGN ++FKPSE TP  G+ +  LW+ AGLP  V
Sbjct: 123 PHGVLAVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHV 182

Query: 194 LNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEMGGNNPLIID 253
           L +V GG E G+AL   E LDG+LFTG    G  +HR L+  P KILALE+GGN PL++ 
Sbjct: 183 LTIVIGGGEAGEALVRHEALDGVLFTGGVQAGRAIHRALADAPHKILALELGGNAPLVVW 242

Query: 254 EVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDDE 313
           +VADI+AA HL +QSA+VTAGQRCTCARRL+L  GA+GDA L  L  +  RL  G     
Sbjct: 243 DVADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQS 302

Query: 314 PQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGIIEMTGVAGVPD 373
           P PF+G +I   AA QV+ A  ++ A GGRPL    + +A ++LL+PG+IE+T  A + D
Sbjct: 303 PAPFMGPVIDAHAAAQVLAAQDRMTADGGRPLRLAAVREARSALLSPGLIELTD-APLRD 361

Query: 374 EEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKPL 433
           EE+FGPLL+V R   FD A+ +AN TRFGL+ GL+S +   + +     RAGIVNWN+P 
Sbjct: 362 EEIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPT 421

Query: 434 TGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDS--LTLPATLNP 482
           TGA+S APFGG+G SGNHRPSA+YAADY A+P+A LES S    LP  LNP
Sbjct: 422 TGASSAAPFGGVGGSGNHRPSAYYAADYSAYPVAGLESPSPVYRLPIGLNP 472


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: 718
Number of extensions: 27
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: 492
Length of database: 472
Length adjustment: 34
Effective length of query: 458
Effective length of database: 438
Effective search space:   200604
Effective search space used:   200604
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 CCNA_00618 CCNA_00618 (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.6693.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-195  634.0   1.3     1e-194  633.7   1.3    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00618  CCNA_00618 succinylglutamic semi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00618  CCNA_00618 succinylglutamic semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  633.7   1.3    1e-194    1e-194      14     470 ..       5     460 ..       2     471 .. 0.99

  Alignments for each domain:
  == domain 1  score: 633.7 bits;  conditional E-value: 1e-194
                             TIGR03240  14 slesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviaketg 86 
                                            l s+dp t+e++ + +  +a ++++a+++ar+af++wa ++l+er a+  rfae ++ ++ee+a++ia+etg
  lcl|FitnessBrowser__Caulo:CCNA_00618   5 RLISRDPYTGEAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVRARREEIATLIARETG 77 
                                           56799******************************************************************** PP

                             TIGR03240  87 kplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhivpalla 159
                                           kp+wea te  s++akvaisi+a +er+Ge+++++ada+a l hrphGvlav+Gp+nfp hl nGhivpalla
  lcl|FitnessBrowser__Caulo:CCNA_00618  78 KPMWEALTEADSVAAKVAISIRAQDERAGERSEPMADATARLAHRPHGVLAVIGPFNFPMHLANGHIVPALLA 150
                                           ************************************************************************* PP

                             TIGR03240 160 GntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqlag 232
                                           Gn+vvfkpse tp +++ + +lw++aGlp+ vl +v G+ e+G+al+ +e +dG+lftG  ++G  +hr la+
  lcl|FitnessBrowser__Caulo:CCNA_00618 151 GNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIVIGGGEAGEALVRHEALDGVLFTGGVQAGRAIHRALAD 223
                                           ************************************************************************* PP

                             TIGR03240 233 rpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltv 305
                                            p+kilalelGGn plvv++v+di+aa+hlivqsa+++aGqrctcarrl++++ga+Gdalle+l+ + +rl++
  lcl|FitnessBrowser__Caulo:CCNA_00618 224 APHKILALELGGNAPLVVWDVADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVI 296
                                           ************************************************************************* PP

                             TIGR03240 306 gkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpl 378
                                           g   + p+pf+G+vi ++aa ++laaq++++a gg+ l      e+ +all+pg+i++t+ a + dee fgpl
  lcl|FitnessBrowser__Caulo:CCNA_00618 297 GGPFQSPAPFMGPVIDAHAAAQVLAAQDRMTADGGRPLRLAAVREARSALLSPGLIELTD-APLRDEEIFGPL 368
                                           *9999*********************************9999999***************.699********* PP

                             TIGR03240 379 lkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrp 451
                                           l+v r +dfd+ala an+trfGlaaGl+sdd++ly++f++++raGivnwn+p+tGassaapfGG+G sGnhrp
  lcl|FitnessBrowser__Caulo:CCNA_00618 369 LQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPTTGASSAAPFGGVGGSGNHRP 441
                                           ************************************************************************* PP

                             TIGR03240 452 sayyaadycaypvaslead 470
                                           sayyaady aypva le+ 
  lcl|FitnessBrowser__Caulo:CCNA_00618 442 SAYYAADYSAYPVAGLESP 460
                                           ****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (472 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: 00:00:00.01
# Mc/sec: 11.84
//
[ok]

This GapMind analysis is from Sep 17 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 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