Alignments for a candidate for serA in Phaeacidiphilus oryzae TH49

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Phaeacidiphilus oryzae TH49

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_037572577.1 BS73_RS14720 phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>NCBI__GCF_000744815.1:WP_037572577.1
          Length = 528

 Score =  855 bits (2210), Expect = 0.0
 Identities = 441/525 (84%), Positives = 480/525 (91%)

Query: 4   KPVVLIAEELSPATVDALGPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAVAA 63
           KPVVLIAEELSPATVDALGPDFEIR CNGADRA+LLPA+A+VDA+L+RSATK+DAEA+AA
Sbjct: 2   KPVVLIAEELSPATVDALGPDFEIRTCNGADRAQLLPALAEVDAVLIRSATKMDAEAIAA 61

Query: 64  AKKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQANA 123
           A+ LKV+ARAGVGLDNVDV AATKAGVMVVNAPTSNIVTAAELACGL+++TAR+IP A A
Sbjct: 62  AQNLKVIARAGVGLDNVDVQAATKAGVMVVNAPTSNIVTAAELACGLLISTARHIPAATA 121

Query: 124 ALKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAAQM 183
           ALK GEWKRSKYTGVELAEKTLGVVGLGRIG LVAQRMSAFGMKVVAYDPY+Q ARAAQM
Sbjct: 122 ALKQGEWKRSKYTGVELAEKTLGVVGLGRIGVLVAQRMSAFGMKVVAYDPYIQAARAAQM 181

Query: 184 GVKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEALY 243
           GVK+LSLDELLEVSDFITVHLPKTPETLGLIGDEAL KVKP+VRIVNAARGGIVDE AL 
Sbjct: 182 GVKLLSLDELLEVSDFITVHLPKTPETLGLIGDEALHKVKPTVRIVNAARGGIVDEGALI 241

Query: 244 SALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAVAKSVRLA 303
           SALK+GRVAGAGLDVY+ EPCTDSPLF FD VV TPHLGASTDEAQEKAGIAVAKSVRLA
Sbjct: 242 SALKDGRVAGAGLDVYSSEPCTDSPLFGFDNVVCTPHLGASTDEAQEKAGIAVAKSVRLA 301

Query: 304 LAGELVPDAVNVQGGVIAEDVKPGLPLAERLGRIFTALAGEVAVRLDVEVYGEITQHDVK 363
           LAGELVPDAVNVQGGVIAEDV+PGLPLAERLGRIFTALAGEVAVRLDVEV GEITQHDVK
Sbjct: 302 LAGELVPDAVNVQGGVIAEDVRPGLPLAERLGRIFTALAGEVAVRLDVEVRGEITQHDVK 361

Query: 364 VLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVIVRGTLSDGE 423
           VLELSALKGVFEDVV ETVSYVNAPLFAQERG+EVRLTT+SESP+HRNV+ VRGTL+DG 
Sbjct: 362 VLELSALKGVFEDVVAETVSYVNAPLFAQERGLEVRLTTTSESPDHRNVISVRGTLNDGR 421

Query: 424 EVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGEAGLNIA 483
            VSVSGTL+GPK +QKIV +  +DVD+ L DHM   RY+DRPGVVGT+GRI+G+A +NI 
Sbjct: 422 TVSVSGTLSGPKRIQKIVGVDSFDVDVILTDHMAFFRYQDRPGVVGTLGRILGDAEINIE 481

Query: 484 GMQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSVNL 528
           GMQV+  T  G+AL  LTVD  +P  VLAE+  EIGA  ARSV+L
Sbjct: 482 GMQVSPDTESGDALVSLTVDREIPQPVLAEIVGEIGAKFARSVDL 526


Lambda     K      H
   0.315    0.133    0.362 

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: 1037
Number of extensions: 31
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: 529
Length of database: 528
Length adjustment: 35
Effective length of query: 494
Effective length of database: 493
Effective search space:   243542
Effective search space used:   243542
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 WP_037572577.1 BS73_RS14720 (phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

# 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.aa/TIGR01327.hmm
# target sequence database:        /tmp/gapView.1619221.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01327  [M=525]
Accession:   TIGR01327
Description: PGDH: phosphoglycerate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.2e-187  607.8   3.3     1e-186  607.7   3.3    1.0  1  NCBI__GCF_000744815.1:WP_037572577.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037572577.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.7   3.3    1e-186    1e-186       2     513 ..       5     514 ..       4     526 .. 0.97

  Alignments for each domain:
  == domain 1  score: 607.7 bits;  conditional E-value: 1e-186
                             TIGR01327   2 vlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGvD 74 
                                           vl+a++ls++++++l   ++e+++ +g ++++ll ++ ++da+++RSatk+++e ++aa++Lkvi+RaGvG+D
  NCBI__GCF_000744815.1:WP_037572577.1   5 VLIAEELSPATVDALGP-DFEIRTCNGADRAQLLPALAEVDAVLIRSATKMDAEAIAAAQNLKVIARAGVGLD 76 
                                           9**************95.58***************************************************** PP

                             TIGR01327  75 NidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGlG 147
                                           N+d++aatk G++vvNaP++n+++aaEla  ll++ aR+ip+a++ +k+++W+r+k++G+El +ktlGv+GlG
  NCBI__GCF_000744815.1:WP_037572577.1  77 NVDVQAATKAGVMVVNAPTSNIVTAAELACGLLISTARHIPAATAALKQGEWKRSKYTGVELAEKTLGVVGLG 149
                                           ************************************************************************* PP

                             TIGR01327 148 riGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakmK 220
                                           riG  va+r+ a+gmkv+ayDPyi  ++a+++gv+ll+ ldell+ +D+itvH+P+t+et glig e+l k+K
  NCBI__GCF_000744815.1:WP_037572577.1 150 RIGVLVAQRMSAFGMKVVAYDPYIQAARAAQMGVKLLS-LDELLEVSDFITVHLPKTPETLGLIGDEALHKVK 221
                                           ***********************************666.********************************** PP

                             TIGR01327 221 kgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvavev 293
                                           ++v+ivN+aRGGi+dE AL+ al++g+v++a+lDv+++EP+td++l+ +dnvv tpHlgAst Eaqe++++ v
  NCBI__GCF_000744815.1:WP_037572577.1 222 PTVRIVNAARGGIVDEGALISALKDGRVAGAGLDVYSSEPCTDSPLFGFDNVVCTPHLGASTDEAQEKAGIAV 294
                                           ************************************************************************* PP

                             TIGR01327 294 aeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesellts 366
                                           a++v+ al+ge v++avN+       +e+++p l lae+lG + + l++e   +++v+++Ge++++++++l+ 
  NCBI__GCF_000744815.1:WP_037572577.1 295 AKSVRLALAGELVPDAVNVQG--GVIAEDVRPGLPLAERLGRIFTALAGEVAVRLDVEVRGEITQHDVKVLEL 365
                                           ******************988..778889******************************************** PP

                             TIGR01327 367 allkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkg.evsvagtvlee.kepri 437
                                           ++lkg++++v++e+v +vnA+  a+erg++v+ ++++es+d++n+++v+ + ++g +vsv+gt+ +   +++i
  NCBI__GCF_000744815.1:WP_037572577.1 366 SALKGVFEDVVAETVSYVNAPLFAQERGLEVRLTTTSESPDHRNVISVRGTLNDGrTVSVSGTLSGPkRIQKI 438
                                           ************************************************987665559*******9985789** PP

                             TIGR01327 438 veidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevlee 510
                                           v +d+f+vd+  ++++ +++++D+pGv+g +g++lg+a+iNi +mq++ +++ g+al+ l++D+e+++ vl+e
  NCBI__GCF_000744815.1:WP_037572577.1 439 VGVDSFDVDVILTDHMAFFRYQDRPGVVGTLGRILGDAEINIEGMQVSPDTESGDALVSLTVDREIPQPVLAE 511
                                           ************************************************************************9 PP

                             TIGR01327 511 ike 513
                                           i  
  NCBI__GCF_000744815.1:WP_037572577.1 512 IVG 514
                                           965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (528 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 21.81
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis