Alignments for a candidate for putA in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Trichormus variabilis ATCC 29413

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011319687.1 AVA_RS14900 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_000204075.1:WP_011319687.1
          Length = 993

 Score =  487 bits (1253), Expect = e-142
 Identities = 249/503 (49%), Positives = 327/503 (65%), Gaps = 2/503 (0%)

Query: 11  TDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKDQLVGSVSKA 70
           TDF VE  RK    A   V   LG+ Y  +INGE V T + I S NP+   +++G V   
Sbjct: 479 TDFAVEEERKEAARAFAEVRGALGRSYLPLINGEYVQTAEVIDSVNPSNFGEVIGKVGLI 538

Query: 71  NQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEA 130
           + + AE+A+Q+A  AF  WR    +ERA IL +A  ++  R+ E SAW+V E GKP KEA
Sbjct: 539 SVEQAEQAMQAAKAAFPGWRRTPVKERAAILRRAGDLLEERRAELSAWIVLEVGKPVKEA 598

Query: 131 DADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVG 190
           DA+ +EAIDF  YYA +M  L +G       GE NRY Y P G+ V ISPWNF LAI  G
Sbjct: 599 DAEVSEAIDFCRYYADEMERLYQGINY-DVAGETNRYIYQPRGIVVVISPWNFPLAIACG 657

Query: 191 TAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPK 250
             VA +VTGN  +LKPA T+ V+ AK  E+L +AG+PKGV  YVPG G++VG YLV HP 
Sbjct: 658 MTVAALVTGNCTLLKPAETSSVITAKLTEILLEAGIPKGVFQYVPGKGSQVGAYLVSHPD 717

Query: 251 TSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILV 310
           T LI FTGS++VG R+Y  AA ++P Q H+KRVI EMGGK+ ++VD  ADLD A   ++ 
Sbjct: 718 THLIAFTGSQEVGCRIYAEAATLKPQQRHMKRVIAEMGGKNAIIVDESADLDQAVIGVVQ 777

Query: 311 SAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEK 370
           SAFG+SGQKCSA SR ++ + +YD  + + V   K+L +G+       +GPVID  A ++
Sbjct: 778 SAFGYSGQKCSACSRVIVVEAIYDAFIHRLVEATKSLNIGEAELPSTQVGPVIDANARDR 837

Query: 371 IMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDF 430
           I  YIE GK E ++       +  G+F+ P I  ++ P   I Q+EIFGPV+A  KA DF
Sbjct: 838 IREYIEKGKAESQVALELSAPNH-GYFVGPVIFGEVPPHGTIAQQEIFGPVLAVIKAKDF 896

Query: 431 DHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMS 490
             AL IAN+T+Y LTG + +R  +HI+QA+ EF VGNLY NRN TGAIV   PFGGFK+S
Sbjct: 897 AQALAIANDTDYALTGGLYSRTPSHIQQAQEEFEVGNLYINRNITGAIVARQPFGGFKLS 956

Query: 491 GTDSKAGGPDYLALHMQAKTVSE 513
           G  SKAGGPDYL   ++ +T++E
Sbjct: 957 GVGSKAGGPDYLLQFLEPRTITE 979


Lambda     K      H
   0.316    0.134    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: 1089
Number of extensions: 47
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: 515
Length of database: 993
Length adjustment: 39
Effective length of query: 476
Effective length of database: 954
Effective search space:   454104
Effective search space used:   454104
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: 55 (25.8 bits)

Align candidate WP_011319687.1 AVA_RS14900 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01237 (pruA: putative delta-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/TIGR01237.hmm
# target sequence database:        /tmp/gapView.9187.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01237  [M=511]
Accession:   TIGR01237
Description: D1pyr5carbox2: putative delta-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-247  807.6   2.0   4.3e-247  806.8   2.0    1.3  1  lcl|NCBI__GCF_000204075.1:WP_011319687.1  AVA_RS14900 L-glutamate gamma-se


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011319687.1  AVA_RS14900 L-glutamate gamma-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  806.8   2.0  4.3e-247  4.3e-247       5     511 .]     477     981 ..     475     981 .. 0.99

  Alignments for each domain:
  == domain 1  score: 806.8 bits;  conditional E-value: 4.3e-247
                                 TIGR01237   5 pftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeq 73 
                                                +tdfa ee ++++ +a+a+v+  lG++y+++inGe+v+t++ ids+np++  ev+Gkv+++sve+aeq
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 477 TDTDFAVEEERKEAARAFAEVRGALGRSYLPLINGEYVQTAEVIDSVNPSNFGEVIGKVGLISVEQAEQ 545
                                               68******************************************************************* PP

                                 TIGR01237  74 alqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyar 142
                                               a+qaak+af+ w++t+v+eraail++a + l++rr elsa++vlevGk+++eadaev+eaidf++yya+
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 546 AMQAAKAAFPGWRRTPVKERAAILRRAGDLLEERRAELSAWIVLEVGKPVKEADAEVSEAIDFCRYYAD 614
                                               ********************************************************************* PP

                                 TIGR01237 143 emiklakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaa 211
                                               em++l  ++ + ++ Ge+nry+y+p+G+ vvispwnfplai+ Gmtva++vtGnc++lkpae+++vi+a
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 615 EMERLY-QGINYDVAGETNRYIYQPRGIVVVISPWNFPLAIACGMTVAALVTGNCTLLKPAETSSVITA 682
                                               *****9.99************************************************************ PP

                                 TIGR01237 212 klveileeaGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrvi 280
                                               kl eil eaG+pkGv+q+vpGkGs+vG ylv+hp+t+li+ftGs+evG+riy++aa ++p q+h+krvi
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 683 KLTEILLEAGIPKGVFQYVPGKGSQVGAYLVSHPDTHLIAFTGSQEVGCRIYAEAATLKPQQRHMKRVI 751
                                               ********************************************************************* PP

                                 TIGR01237 281 aelGGkdavivdesadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkvgktd 349
                                               ae+GGk+a+ivdesad++qav ++v+safG++Gqkcsa+srv+v+e +yd++++r+veatksl++g+++
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 752 AEMGGKNAIIVDESADLDQAVIGVVQSAFGYSGQKCSACSRVIVVEAIYDAFIHRLVEATKSLNIGEAE 820
                                               ********************************************************************* PP

                                 TIGR01237 350 eadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeifGpvv 418
                                                +++qvgpvid+++ d+i+eyie gkae++++l   +++++Gyf++p if++v ++ ++aq+eifGpv+
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 821 LPSTQVGPVIDANARDRIREYIEKGKAESQVALE-LSAPNHGYFVGPVIFGEVPPHGTIAQQEIFGPVL 888
                                               *********************************9.99******************************** PP

                                 TIGR01237 419 avlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGfkmsG 487
                                               av++akdf +al ian+t+y+ltGg++s+++ +i++a++efevGnly+nr+itGaiv++qpfGGfk+sG
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 889 AVIKAKDFAQALAIANDTDYALTGGLYSRTPSHIQQAQEEFEVGNLYINRNITGAIVARQPFGGFKLSG 957
                                               ********************************************************************* PP

                                 TIGR01237 488 tdskaGGpdylaqflqaktvteri 511
                                               ++skaGGpdyl+qfl+++t+te+i
  lcl|NCBI__GCF_000204075.1:WP_011319687.1 958 VGSKAGGPDYLLQFLEPRTITENI 981
                                               **********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (993 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 20.97
//
[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)
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SQLite3 databases

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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