Alignments for a candidate for serA in Hippea alviniae EP5-r

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Hippea alviniae EP5-r

Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_022671272.1 G415_RS0108550 phosphoglycerate dehydrogenase

Query= uniprot:Q5JGC4
         (304 letters)



>NCBI__GCF_000420385.1:WP_022671272.1
          Length = 529

 Score =  236 bits (602), Expect = 9e-67
 Identities = 123/306 (40%), Positives = 197/306 (64%), Gaps = 4/306 (1%)

Query: 2   KVLVAAPLHEKAIEVLKNA-GFEVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEA 60
           KV++   + E  I++L+N    EV  +   D+  L + ++D DAII RS   + ++ +  
Sbjct: 3   KVVICDNISEAGIDILRNEPDIEVEIKSDVDKKELPKQLEDADAIITRSSTTIDKEFLSY 62

Query: 61  APKLKVIGRAGVGLDNIDLKAAEERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADR 120
              LKVIGRAGVG+DNIDL+ A ++GI V+N P  ++ +  E  +  I    R +  A+ 
Sbjct: 63  CKNLKVIGRAGVGVDNIDLEEASKKGIVVLNMPTGNTLAATEHTMTFILNCLRFMPNANY 122

Query: 121 KMR-EGVWAKKQCMGIELEGKTIGVVGFGRIGYQVAKIANALGMKVLFYDPYPNEERAKE 179
           +++ + +W +K+ MGIEL GKT+G++G GRIG +VA    + G  V+ YDPY  +E+A +
Sbjct: 123 ELKYKHIWDRKKWMGIELYGKTVGIIGMGRIGTRVAIRVMSFGANVIVYDPYIPKEKATK 182

Query: 180 VGGKFAD-LETLLKESDVVTLHVPLVDATYHLINEERLKLMKPTAILINAARGAVVDTDA 238
           +G K  D L+ L++ +D++T+H P  + TY++I++E ++ MK   ILIN ARG + +  A
Sbjct: 183 IGAKIVDDLDELIRNADIITIHTPKTNETYNMIDKEEIEKMKDGVILINCARGGLYNEKA 242

Query: 239 LVKALQEGWIAGAGLDVFEEEPLPADHPLTKLDNVVLTPHIGASTVEAQMRAGVEVAEKI 298
           L + L+   I   G+DVFE EP P +HPL + DNV+ TPH+GA+T E+Q+R G  +A+ +
Sbjct: 243 LYEGLKSRKIRALGIDVFENEPQP-NHPLLEFDNVIATPHLGANTYESQVRVGEGIAKSV 301

Query: 299 VEALKG 304
           ++ALKG
Sbjct: 302 IDALKG 307


Lambda     K      H
   0.317    0.136    0.378 

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: 437
Number of extensions: 26
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: 304
Length of database: 529
Length adjustment: 31
Effective length of query: 273
Effective length of database: 498
Effective search space:   135954
Effective search space used:   135954
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: 50 (23.9 bits)

Align candidate WP_022671272.1 G415_RS0108550 (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.1441168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-200  652.2   5.1   3.8e-200  652.0   5.1    1.0  1  NCBI__GCF_000420385.1:WP_022671272.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022671272.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  652.0   5.1  3.8e-200  3.8e-200       1     525 []       3     529 .]       3     529 .] 0.98

  Alignments for each domain:
  == domain 1  score: 652.0 bits;  conditional E-value: 3.8e-200
                             TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvG 72 
                                           kv+++d++se+gi+ l +e ++ev++k++++k+el ++++d+da+i+RS+t++++e+l+  ++LkvigRaGvG
  NCBI__GCF_000420385.1:WP_022671272.1   3 KVVICDNISEAGIDiLRNEPDIEVEIKSDVDKKELPKQLEDADAIITRSSTTIDKEFLSYCKNLKVIGRAGVG 75 
                                           79************6667789**************************************************** PP

                             TIGR01327  73 vDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekk.WerkkflGtElygktlGvi 144
                                           vDNid+e+a+kkGi+v+N P+gnt++a+E++++ +l+  R +p+a+ ++k k+ W+rkk++G+Elygkt+G+i
  NCBI__GCF_000420385.1:WP_022671272.1  76 VDNIDLEEASKKGIVVLNMPTGNTLAATEHTMTFILNCLRFMPNANYELKYKHiWDRKKWMGIELYGKTVGII 148
                                           **************************************************9888******************* PP

                             TIGR01327 145 GlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeela 217
                                           G+GriG++va r+ ++g++v++yDPyi++eka+k+g + ++dldel+++aD+it+H+P+t+et ++i+kee++
  NCBI__GCF_000420385.1:WP_022671272.1 149 GMGRIGTRVAIRVMSFGANVIVYDPYIPKEKATKIGAKIVDDLDELIRNADIITIHTPKTNETYNMIDKEEIE 221
                                           ************************************************************************* PP

                             TIGR01327 218 kmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenva 290
                                           kmK+gvi++NcaRGG+++EkAL+e l++ k+ra+++Dvfe+EP  +++lle+dnv++tpHlgA+t+E+q +v+
  NCBI__GCF_000420385.1:WP_022671272.1 222 KMKDGVILINCARGGLYNEKALYEGLKSRKIRALGIDVFENEPQPNHPLLEFDNVIATPHLGANTYESQVRVG 294
                                           ************************************************************************* PP

                             TIGR01327 291 vevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesel 363
                                             +a++v++alkg   e+avN+ + ++e +e  k +l lae++G++ sq++k+ ++k++v  +Ge+ + + + 
  NCBI__GCF_000420385.1:WP_022671272.1 295 EGIAKSVIDALKGRGYENAVNIKMEEEEITELGKQFLGLAERMGSFLSQYVKSFIRKITVYAHGEIESCT-NS 366
                                           **********************99888888889*********************************9998.88 PP

                             TIGR01327 364 ltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkg.evsvagtvleekep 435
                                           l  +   g+lk++++e+vn+vnA+++akerg+++e +  ++++++kn+l + +e d++ + +++gtv+e ++ 
  NCBI__GCF_000420385.1:WP_022671272.1 367 LGLFTTVGILKNMVDEHVNYVNAPYLAKERGLEIETKIYDKATEFKNYLLISAEYDDDkTLEIGGTVFEPNKA 439
                                           9999*************************************************98776489************ PP

                             TIGR01327 436 riveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevl 508
                                           riv +dgf++++e +g +++++n+DkpG+igkvg++lg+++iNia+++lgrk++ geal  +++D++vse +l
  NCBI__GCF_000420385.1:WP_022671272.1 440 RIVYMDGFDMEIELTGNIIVFRNHDKPGIIGKVGEILGRHNINIADFRLGRKKETGEALSFIKVDQDVSEAIL 512
                                           ************************************************************************* PP

                             TIGR01327 509 eeikevpeiksvklvel 525
                                           +ei +++ + s++ v+l
  NCBI__GCF_000420385.1:WP_022671272.1 513 KEIWNIDGAISISKVRL 529
                                           ***********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (529 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.69
//
[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