Alignments for a candidate for putA in Trichodesmium erythraeum IMS101

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Trichodesmium erythraeum IMS101

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011612882.1 TERY_RS16535 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_000014265.1:WP_011612882.1
          Length = 993

 Score =  480 bits (1236), Expect = e-140
 Identities = 240/503 (47%), Positives = 327/503 (65%), Gaps = 2/503 (0%)

Query: 11  TDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKDQLVGSVSKA 70
           +D+     R+     +G +  ELGK Y  IINGE   T   + S NP+   ++VG +   
Sbjct: 478 SDYANFQQRQQALNTIGQIRLELGKTYLPIINGEYTNTAQIVDSLNPSNSKEVVGKIGLI 537

Query: 71  NQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEA 130
           + + AE+AIQ+A  AF +W+     ER  IL KAA ++ +R+HE +AW+V E GKP  + 
Sbjct: 538 SVEQAEQAIQAAKAAFPSWKKTPVRERTRILRKAADLMEKRRHELAAWMVLEVGKPLNQG 597

Query: 131 DADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVG 190
           +A+ +EAIDF  YYA +M  L +G       GE +RY+Y P G+++ ISPWNF LAI  G
Sbjct: 598 NAEVSEAIDFCRYYADEMERLEQGYNY-DVAGETDRYYYQPRGISLVISPWNFPLAIPTG 656

Query: 191 TAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPK 250
             V+ +VTGN  +LKPA+ + V+A+K  E+L +AG PKGV  +VPG+G+ VGD++V HP 
Sbjct: 657 MTVSSLVTGNCTLLKPAAVSSVIASKISEILLEAGFPKGVFQFVPGNGSTVGDFMVKHPS 716

Query: 251 TSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILV 310
            + ITFTGS +VG  +Y +AAV++P Q HLKRVI EMGGK+ ++VD  ADLD A   ++ 
Sbjct: 717 VNSITFTGSMEVGCHIYAQAAVLQPRQKHLKRVIAEMGGKNAIIVDESADLDQAVAGVVY 776

Query: 311 SAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEK 370
           SAFG+SGQKCSA SR V+   +YD  + + V   ++L +GD       +GPVIDEKA ++
Sbjct: 777 SAFGYSGQKCSACSRVVVLATIYDSFVNRLVEATRSLNIGDAEKPSTQVGPVIDEKAQKR 836

Query: 371 IMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDF 430
           I  YI  GK+E  +          G+F+ P I  D+ P A I QEEIFGPV+A  KA++F
Sbjct: 837 IQEYIVKGKQEAEVAIEMSAPKD-GYFVGPVIFKDVSPSATIAQEEIFGPVLAVMKADNF 895

Query: 431 DHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMS 490
             ALEIAN T + LTG + +R  +HIEQAK EF VGNLY NR  TGAIV   PFGGFK+S
Sbjct: 896 TQALEIANGTNFALTGGLYSRTPSHIEQAKAEFEVGNLYINRGITGAIVSRQPFGGFKLS 955

Query: 491 GTDSKAGGPDYLALHMQAKTVSE 513
           G  SKAGGPDYL   ++ +T++E
Sbjct: 956 GVGSKAGGPDYLLQFLEPRTITE 978


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: 1118
Number of extensions: 41
Number of successful extensions: 3
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_011612882.1 TERY_RS16535 (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.405.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-245  802.2   0.9   1.4e-245  801.8   0.9    1.1  1  lcl|NCBI__GCF_000014265.1:WP_011612882.1  TERY_RS16535 L-glutamate gamma-s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011612882.1  TERY_RS16535 L-glutamate gamma-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  801.8   0.9  1.4e-245  1.4e-245       3     511 .]     474     980 ..     472     980 .. 0.99

  Alignments for each domain:
  == domain 1  score: 801.8 bits;  conditional E-value: 1.4e-245
                                 TIGR01237   3 nepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasveda 71 
                                               n+ ++d+a+ +++q++ +++ +++  lGk+y+++inGe+ +t++ +ds+np++++evvGk++++sve+a
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 474 NAADSDYANFQQRQQALNTIGQIRLELGKTYLPIINGEYTNTAQIVDSLNPSNSKEVVGKIGLISVEQA 542
                                               677899*************************************************************** PP

                                 TIGR01237  72 eqalqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyy 140
                                               eqa+qaak+af++wkkt+v+er++il+kaa+ +++rrhel+a++vlevGk++++ +aev+eaidf++yy
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 543 EQAIQAAKAAFPSWKKTPVRERTRILRKAADLMEKRRHELAAWMVLEVGKPLNQGNAEVSEAIDFCRYY 611
                                               ********************************************************************* PP

                                 TIGR01237 141 aremiklakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatvi 209
                                               a+em++l+ ++ + ++ Ge++ry y+p+G+++vispwnfplai  Gmtv+++vtGnc++lkpa  ++vi
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 612 ADEMERLE-QGYNYDVAGETDRYYYQPRGISLVISPWNFPLAIPTGMTVSSLVTGNCTLLKPAAVSSVI 679
                                               *******9.99********************************************************** PP

                                 TIGR01237 210 aaklveileeaGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkr 278
                                               a+k+ eil eaG pkGv+qfvpG+Gs vG+++v+hp ++ itftGs evG++iy++aa +qp qkhlkr
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 680 ASKISEILLEAGFPKGVFQFVPGNGSTVGDFMVKHPSVNSITFTGSMEVGCHIYAQAAVLQPRQKHLKR 748
                                               ********************************************************************* PP

                                 TIGR01237 279 viaelGGkdavivdesadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkvgk 347
                                               viae+GGk+a+ivdesad++qava++v+safG++Gqkcsa+srvvvl ++yd +v+r+veat+sl++g 
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 749 VIAEMGGKNAIIVDESADLDQAVAGVVYSAFGYSGQKCSACSRVVVLATIYDSFVNRLVEATRSLNIGD 817
                                               ********************************************************************* PP

                                 TIGR01237 348 tdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeifGp 416
                                               ++++++qvgpvid+k++++i+eyi  gk+e+++++  ++++++Gyf++p ifkdv + a++aqeeifGp
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 818 AEKPSTQVGPVIDEKAQKRIQEYIVKGKQEAEVAIE-MSAPKDGYFVGPVIFKDVSPSATIAQEEIFGP 885
                                               ***********************************9.99****************************** PP

                                 TIGR01237 417 vvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGfkm 485
                                               v+av++a +f +aleian+t+++ltGg++s+++ +ie+akaefevGnly+nr itGaiv++qpfGGfk+
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 886 VLAVMKADNFTQALEIANGTNFALTGGLYSRTPSHIEQAKAEFEVGNLYINRGITGAIVSRQPFGGFKL 954
                                               ********************************************************************* PP

                                 TIGR01237 486 sGtdskaGGpdylaqflqaktvteri 511
                                               sG++skaGGpdyl+qfl+++t+te+i
  lcl|NCBI__GCF_000014265.1:WP_011612882.1 955 SGVGSKAGGPDYLLQFLEPRTITENI 980
                                               ************************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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 17.36
//
[ok]

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

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