Alignments for a candidate for putA in Crocosphaera subtropica ATCC 51142

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Crocosphaera subtropica ATCC 51142

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_009544399.1 CCE_RS07540 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_000017845.1:WP_009544399.1
          Length = 990

 Score =  494 bits (1273), Expect = e-144
 Identities = 251/509 (49%), Positives = 335/509 (65%), Gaps = 2/509 (0%)

Query: 5   YKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKDQLV 64
           + + P TD++ E  R+  ++AL  V+  LGK Y  +INGE V T+  I S NP++  ++V
Sbjct: 470 FVNAPDTDYSREVLREKAQQALVKVKDSLGKTYLPLINGEYVQTDVIIDSLNPSKSSEVV 529

Query: 65  GSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAG 124
           G +   + + AE+A+ +A EAF+ W+     ERA IL KA  ++  R+HE SAW+  E G
Sbjct: 530 GQIGLISIEQAEQALNAAKEAFKDWKKTPATERARILRKAGDLMEERRHELSAWICVEVG 589

Query: 125 KPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFA 184
           K  ++ADA+ +EAIDF  YYA +M  L++G       GE NRY Y P G+ + ISPWNF 
Sbjct: 590 KILQQADAEVSEAIDFCRYYADEMERLDKGYNY-DVAGETNRYHYQPRGIALVISPWNFP 648

Query: 185 LAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDY 244
            AI  G  VA +VTGN  +LKPA T+ V+AAK  E+L DAG+PKGV   VPG G++VG Y
Sbjct: 649 FAIATGMTVAALVTGNCTLLKPAETSTVIAAKIAEILVDAGIPKGVFQLVPGKGSKVGAY 708

Query: 245 LVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLA 304
           +V+HP   LI FTGS++VG R+Y  AA+++PGQ HLKRVI EMGGK+ ++VD  ADLD A
Sbjct: 709 MVNHPDVHLIAFTGSREVGCRIYADAAILQPGQKHLKRVIAEMGGKNAIIVDESADLDQA 768

Query: 305 AESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVID 364
               + SAFG++GQKCSA SR ++   VYD  LE+ V   K+L VG        +GPVID
Sbjct: 769 VAGAVFSAFGYTGQKCSAASRIIVLDPVYDAFLERFVDATKSLNVGPTDEPSTQVGPVID 828

Query: 365 EKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAF 424
             A ++I+ YIE  K+E  L    E   + GF++ PTI  D+ P   I QEEIFGPVVA 
Sbjct: 829 ATAQKRILEYIETAKQESTLALAMEAPDN-GFYVGPTIFGDVLPNHTIAQEEIFGPVVAV 887

Query: 425 SKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPF 484
            +  +FD ALE+AN T+Y LTG + +R+  HIEQA++EF VGNLY NR  TGAIV   PF
Sbjct: 888 MRVKNFDEALEVANGTDYALTGGLYSRSPEHIEQAQKEFEVGNLYINRTITGAIVARQPF 947

Query: 485 GGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
           GGFK+SG  SKAGGPDYL   ++ + +SE
Sbjct: 948 GGFKLSGVGSKAGGPDYLLQFLEPRHISE 976


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: 1163
Number of extensions: 51
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: 990
Length adjustment: 39
Effective length of query: 476
Effective length of database: 951
Effective search space:   452676
Effective search space used:   452676
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_009544399.1 CCE_RS07540 (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.18643.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-263  861.0   0.9   1.6e-263  861.0   0.9    1.6  2  lcl|NCBI__GCF_000017845.1:WP_009544399.1  CCE_RS07540 L-glutamate gamma-se


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009544399.1  CCE_RS07540 L-glutamate gamma-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1     0.055     0.055      99     148 ..     137     186 ..     107     199 .. 0.61
   2 !  861.0   0.9  1.6e-263  1.6e-263       3     511 .]     472     978 ..     470     978 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.055
                                 TIGR01237  99 kaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremikla 148
                                               k+ + l++ ++ ++  l  e+  + +ea a     +d++e  a++  k++
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 137 KTVERLRKEKMGFTIDLLGEAVITESEAKAYLDSYLDLMEKLADQSKKWS 186
                                               55566666666666666666666666666666666666666666666655 PP

  == domain 2  score: 861.0 bits;  conditional E-value: 1.6e-263
                                 TIGR01237   3 nepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasveda 71 
                                               n+p+td++ e l++++++al kvk+ lGk+y+++inGe+v+t+  ids+np+++sevvG+++++s+e+a
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 472 NAPDTDYSREVLREKAQQALVKVKDSLGKTYLPLINGEYVQTDVIIDSLNPSKSSEVVGQIGLISIEQA 540
                                               89******************************************************************* PP

                                 TIGR01237  72 eqalqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyy 140
                                               eqal+aak+af++wkkt+  era+il+ka + +++rrhelsa++++evGki+++adaev+eaidf++yy
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 541 EQALNAAKEAFKDWKKTPATERARILRKAGDLMEERRHELSAWICVEVGKILQQADAEVSEAIDFCRYY 609
                                               ********************************************************************* PP

                                 TIGR01237 141 aremiklakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatvi 209
                                               a+em++l+ ++ + ++ Ge+nry y+p+G+a+vispwnfp+ai+ Gmtva++vtGnc++lkpae++tvi
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 610 ADEMERLD-KGYNYDVAGETNRYHYQPRGIALVISPWNFPFAIATGMTVAALVTGNCTLLKPAETSTVI 677
                                               ********.78999******************************************************* PP

                                 TIGR01237 210 aaklveileeaGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkr 278
                                               aak++eil +aG+pkGv+q vpGkGs+vG y+v+hp+++li+ftGsrevG+riy+daa +qpGqkhlkr
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 678 AAKIAEILVDAGIPKGVFQLVPGKGSKVGAYMVNHPDVHLIAFTGSREVGCRIYADAAILQPGQKHLKR 746
                                               ********************************************************************* PP

                                 TIGR01237 279 viaelGGkdavivdesadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkvgk 347
                                               viae+GGk+a+ivdesad++qava+av safG++Gqkcsaasr++vl++vyd+++erfv+atksl+vg+
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 747 VIAEMGGKNAIIVDESADLDQAVAGAVFSAFGYTGQKCSAASRIIVLDPVYDAFLERFVDATKSLNVGP 815
                                               ********************************************************************* PP

                                 TIGR01237 348 tdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeifGp 416
                                               tde+++qvgpvid++++++i eyie +k+e+ l+l+ ++++++G++++ptif+dv ++ ++aqeeifGp
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 816 TDEPSTQVGPVIDATAQKRILEYIETAKQESTLALA-MEAPDNGFYVGPTIFGDVLPNHTIAQEEIFGP 883
                                               ************************************.999***************************** PP

                                 TIGR01237 417 vvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGfkm 485
                                               vvav+r+k+fdeale+an+t+y+ltGg++s+s+e+ie+a++efevGnly+nr+itGaiv++qpfGGfk+
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 884 VVAVMRVKNFDEALEVANGTDYALTGGLYSRSPEHIEQAQKEFEVGNLYINRTITGAIVARQPFGGFKL 952
                                               ********************************************************************* PP

                                 TIGR01237 486 sGtdskaGGpdylaqflqaktvteri 511
                                               sG++skaGGpdyl+qfl++++++e+i
  lcl|NCBI__GCF_000017845.1:WP_009544399.1 953 SGVGSKAGGPDYLLQFLEPRHISENI 978
                                               ************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (990 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 13.89
//
[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