Alignments for a candidate for serA in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Rhodospirillum centenum SW SW; ATCC 51521

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_012566968.1 RC1_RS08565 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_000016185.1:WP_012566968.1
          Length = 525

 Score =  414 bits (1063), Expect = e-120
 Identities = 224/526 (42%), Positives = 334/526 (63%), Gaps = 7/526 (1%)

Query: 1   MFRVLVSDKMSNDGLQPLIESDFIEIVQKNVADAEDELHT----FDALLVRSATKVTEDL 56
           M +VL+SD +S   ++ + +   IE+  K      DEL      +D L +RS+TKVT+D+
Sbjct: 1   MPKVLISDSLSPRAVE-IFKERGIEVDVKTGLKP-DELKAIIGGYDGLAIRSSTKVTKDV 58

Query: 57  FNKMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQ 116
               T+L++VGRAG+GVDN+D+  AT  GV+V+N P GN+I+TAEH  AM+ +L R IP+
Sbjct: 59  LAVATNLRVVGRAGIGVDNVDVPAATARGVVVMNTPFGNSITTAEHAIAMMMALARDIPE 118

Query: 117 ANISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERA 176
           AN S  + +W +  ++G ELYGKTLG++G G IGS +A R     M V  FDPFL+ ERA
Sbjct: 119 ANASTHAGKWEKNRFMGVELYGKTLGVIGCGNIGSIVADRALGLKMKVVAFDPFLSPERA 178

Query: 177 KKIGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEA 236
           + +GV     +E+L  AD IT+HTPLT ET+ +LN++++A+TKKGVR+INCARGG+I E 
Sbjct: 179 QDLGVEKVELDELLRRADFITLHTPLTNETRAILNRDSLARTKKGVRIINCARGGLIVEE 238

Query: 237 ALLEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEV 296
            L  A+E+GHVAGAALDVF  EP   N L     VI TPHLGAST EAQ NVA QV+E++
Sbjct: 239 DLKAAIESGHVAGAALDVFAEEPAKQNGLFGMERVICTPHLGASTTEAQENVALQVAEQM 298

Query: 297 LQFAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIA 356
             +     V++A+N+P+++ ++  +++PY ++A ++GS   Q  +  ++ V +++EG +A
Sbjct: 299 ADYLVSGAVVNALNMPSVSAEDAPRLRPYMKLAEQLGSFAGQITETGLKAVTVEFEGQVA 358

Query: 357 KLETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVT 416
           +L T  +T  +L G L P ++S VN VNA  +A+ER I  SE        Y   I V V+
Sbjct: 359 ELNTRPLTAVVLKGLLAPLMES-VNMVNAPVIAREREIKVSETKRQDAGDYQTLIRVIVS 417

Query: 417 GDRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDI 476
            +  T T+  T       R+VEI    I+   T ++++I+++D  G IG++G  LGD  +
Sbjct: 418 TEARTRTLAGTLFGGDKPRLVEIEDVPIEAEVTPNMLFIRNEDKPGFIGKLGTALGDAGV 477

Query: 477 NIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLI 522
           NIAT  +GR   G  AI ++  D+ L D +V+ +  +P +V  K +
Sbjct: 478 NIATFHLGRTAAGETAIALVCVDQPLGDDLVERIRALPSVVRAKAL 523


Lambda     K      H
   0.317    0.134    0.374 

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: 602
Number of extensions: 14
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: 525
Length of database: 525
Length adjustment: 35
Effective length of query: 490
Effective length of database: 490
Effective search space:   240100
Effective search space used:   240100
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_012566968.1 RC1_RS08565 (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.3694586.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-212  692.1   3.1   3.1e-212  691.9   3.1    1.0  1  NCBI__GCF_000016185.1:WP_012566968.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016185.1:WP_012566968.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.9   3.1  3.1e-212  3.1e-212       1     523 [.       3     523 ..       3     525 .] 0.99

  Alignments for each domain:
  == domain 1  score: 691.9 bits;  conditional E-value: 3.1e-212
                             TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           kvl++d+ls++++e++ke+++evdvktgl+ +el ++i  yd+l +RS+tkvt+++l+ a++L+v+gRaG+Gv
  NCBI__GCF_000016185.1:WP_012566968.1   3 KVLISDSLSPRAVEIFKERGIEVDVKTGLKPDELKAIIGGYDGLAIRSSTKVTKDVLAVATNLRVVGRAGIGV 75 
                                           7************************************************************************ PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146
                                           DN+d++aat++G++v+N+P gn+i++aE+a+a+++alaR+ip+a++s++++kWe+++f+G+ElygktlGviG 
  NCBI__GCF_000016185.1:WP_012566968.1  76 DNVDVPAATARGVVVMNTPFGNSITTAEHAIAMMMALARDIPEANASTHAGKWEKNRFMGVELYGKTLGVIGC 148
                                           ************************************************************************* PP

                             TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219
                                           G+iGs+va+ra +l+mkv+a+DP++s+e+a++lgve+++ ldell++aD+it+H+Plt+et+ ++++++la++
  NCBI__GCF_000016185.1:WP_012566968.1 149 GNIGSIVADRALGLKMKVVAFDPFLSPERAQDLGVEKVE-LDELLRRADFITLHTPLTNETRAILNRDSLART 220
                                           ************************************666.********************************* PP

                             TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvave 292
                                           Kkgv+i+NcaRGG+i E+ L  a+e+g+v++aalDvf++EP+++n l+ +++v+ tpHlgAst+Eaqenva++
  NCBI__GCF_000016185.1:WP_012566968.1 221 KKGVRIINCARGGLIVEEDLKAAIESGHVAGAALDVFAEEPAKQNGLFGMERVICTPHLGASTTEAQENVALQ 293
                                           ************************************************************************* PP

                             TIGR01327 293 vaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesellt 365
                                           vae++ ++l   +v +a+N+p+++ae++ +l+py++lae+lG++a+q++++  k+v+v++eG++ae ++ +lt
  NCBI__GCF_000016185.1:WP_012566968.1 294 VAEQMADYLVSGAVVNALNMPSVSAEDAPRLRPYMKLAEQLGSFAGQITETGLKAVTVEFEGQVAELNTRPLT 366
                                           ************************************************************************* PP

                             TIGR01327 366 sallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriv 438
                                           + +lkgll + +e +vn+vnA+++a+er+i+v+e+k++++ dy++l++v v+++  ++++agt++++++pr+v
  NCBI__GCF_000016185.1:WP_012566968.1 367 AVVLKGLLAPLME-SVNMVNAPVIAREREIKVSETKRQDAGDYQTLIRVIVSTEARTRTLAGTLFGGDKPRLV 438
                                           *********9887.9********************************************************** PP

                             TIGR01327 439 eidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleei 511
                                           ei+++ ++ e +  +l+i+n+DkpG+igk+g++lg+ag+Nia+++lgr+++g+ a++l+ +D+++ ++++e+i
  NCBI__GCF_000016185.1:WP_012566968.1 439 EIEDVPIEAEVTPNMLFIRNEDKPGFIGKLGTALGDAGVNIATFHLGRTAAGETAIALVCVDQPLGDDLVERI 511
                                           ************************************************************************* PP

                             TIGR01327 512 kevpeiksvklv 523
                                           +++p++ ++k++
  NCBI__GCF_000016185.1:WP_012566968.1 512 RALPSVVRAKAL 523
                                           ******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (525 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.00
//
[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