Alignments for a candidate for serA in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Leptospirillum ferrooxidans C2-3

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_014449375.1 LFE_RS06195 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_000284315.1:WP_014449375.1
          Length = 535

 Score =  447 bits (1149), Expect = e-130
 Identities = 232/528 (43%), Positives = 346/528 (65%), Gaps = 7/528 (1%)

Query: 3   RVLVSDKMSNDGLQPLIESDFIEIVQKNVADAED---ELHTFDALLVRSATKVTEDLFNK 59
           RVLVSD +S DGL+   E+ F E+V K     E+   E+  +D L++RS TKVT+D+   
Sbjct: 6   RVLVSDAISEDGLKIFREAGF-EVVVKTKLTPEELAVEIAGYDGLVIRSGTKVTKDILKG 64

Query: 60  MTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANI 119
              LK+VGRAG G+DN+D+D AT HG++V+N P GNTI+TAEHT +++ S+ R IPQAN 
Sbjct: 65  AKRLKVVGRAGAGLDNVDLDAATSHGIVVMNTPGGNTITTAEHTMSLLMSMARRIPQANA 124

Query: 120 SVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKKI 179
           S +S +W ++ ++G EL+ KTLGI+G+G+IG  + Q      M V  FDP+LT E A+K 
Sbjct: 125 SNRSGKWEKSKFMGVELFQKTLGIIGMGKIGQHLTQIAKGLSMHVIAFDPYLTPEVAEKS 184

Query: 180 GVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALL 239
           GV   + +E+ + +D I+VHTPL  ET  L+NK TIAK KKGV ++NCARGGI++E  L 
Sbjct: 185 GVTPVSLDEIYQKSDFISVHTPLNAETTNLINKTTIAKMKKGVYIVNCARGGIVNETDLA 244

Query: 240 EALENGHVAGAALDVFEVEP-PVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298
           EAL +GHVAGAA DVF  EP P D+ L+     I+TPH+GA+TKEAQ NVA  ++++++ 
Sbjct: 245 EALLSGHVAGAAFDVFVQEPVPADHPLLKIDSFISTPHIGAATKEAQENVALAIADQMVD 304

Query: 299 F-AKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAK 357
           + AKG+ +  A NLP+++ +E + + PY ++A  +G+++SQ    P+  V I+Y G IA 
Sbjct: 305 YLAKGV-IRYAANLPSVSPEEMSIVTPYQKLAEIMGNIISQISSSPLSKVTIEYSGEIAT 363

Query: 358 LETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTG 417
           + T+ +T + L G L P +D+ VNEVNA  +AKERGI   E  S+    Y   +S+K++ 
Sbjct: 364 VPTAAVTISALKGILSPILDTMVNEVNAPILAKERGIEVVEVRSTHNGDYTGLLSIKISS 423

Query: 418 DRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDIN 477
                 ++ +       RIV ++   ++  P   ++Y+ +QD  GV+G VG ILG++ IN
Sbjct: 424 PTDFHQISGSVFQKRDYRIVSMDQLPVEVIPEPIMIYLTNQDQPGVVGAVGTILGNHKIN 483

Query: 478 IATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLIDLP 525
           I+ MQ GR   GG+AI M+  D  +   ++ EL  +P+I+S+K++ LP
Sbjct: 484 ISRMQFGRDYPGGKAISMIGVDNEISPALLSELRKIPNILSLKILHLP 531


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: 672
Number of extensions: 28
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: 525
Length of database: 535
Length adjustment: 35
Effective length of query: 490
Effective length of database: 500
Effective search space:   245000
Effective search space used:   245000
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_014449375.1 LFE_RS06195 (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.18134.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-199  647.4   4.3   1.1e-198  647.2   4.3    1.0  1  lcl|NCBI__GCF_000284315.1:WP_014449375.1  LFE_RS06195 phosphoglycerate deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000284315.1:WP_014449375.1  LFE_RS06195 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.2   4.3  1.1e-198  1.1e-198       1     524 [.       6     529 ..       6     530 .. 0.99

  Alignments for each domain:
  == domain 1  score: 647.2 bits;  conditional E-value: 1.1e-198
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               +vlv+d +se+g+++++e ++ev vkt+l+ eel  +i  yd+l++RS tkvt+++l+ a++Lkv+gRa
  lcl|NCBI__GCF_000284315.1:WP_014449375.1   6 RVLVSDAISEDGLKIFREAGFEVVVKTKLTPEELAVEIAGYDGLVIRSGTKVTKDILKGAKRLKVVGRA 74 
                                               79******************************************************************* PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               G G+DN+d++aat +Gi+v+N+P gnti++aE+++ ll+++aR+ipqa++s +++kWe++kf+G+El++
  lcl|NCBI__GCF_000284315.1:WP_014449375.1  75 GAGLDNVDLDAATSHGIVVMNTPGGNTITTAEHTMSLLMSMARRIPQANASNRSGKWEKSKFMGVELFQ 143
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               ktlG+iG+G+iG+++++ ak+l m+v+a+DPy+++e aek gv+   +lde+ +++D+i+vH+Pl+ et
  lcl|NCBI__GCF_000284315.1:WP_014449375.1 144 KTLGIIGMGKIGQHLTQIAKGLSMHVIAFDPYLTPEVAEKSGVTP-VSLDEIYQKSDFISVHTPLNAET 211
                                               ********************************************5.55********************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt.dnklleldnvvvt 275
                                                +li+k ++akmKkgv+ivNcaRGGi++E  L+eal +g+v++aa+Dvf +EP+  d++ll+ d  + t
  lcl|NCBI__GCF_000284315.1:WP_014449375.1 212 TNLINKTTIAKMKKGVYIVNCARGGIVNETDLAEALLSGHVAGAAFDVFVQEPVPaDHPLLKIDSFIST 280
                                               *****************************************************87699*********** PP

                                 TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344
                                               pH+gA t+Eaqenva+ +a++++++l+  v ++a Nlp+++ ee++ + py +lae +G+++sq++++ 
  lcl|NCBI__GCF_000284315.1:WP_014449375.1 281 PHIGAATKEAQENVALAIADQMVDYLAKGVIRYAANLPSVSPEEMSIVTPYQKLAEIMGNIISQISSSP 349
                                               ********************************************************************* PP

                                 TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413
                                                +kv+++++Ge+a+  + ++t ++lkg+l+++l++ vn vnA+++akergi+v e ++ ++ dy+ ll+
  lcl|NCBI__GCF_000284315.1:WP_014449375.1 350 LSKVTIEYSGEIATVPTAAVTISALKGILSPILDTMVNEVNAPILAKERGIEVVEVRSTHNGDYTGLLS 418
                                               ********************************************************************* PP

                                 TIGR01327 414 vkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482
                                               +k+++ ++ ++++g+v+++  +riv +d+  v++ pe i+++++n+D+pGv+g vg++lg++ iNi  m
  lcl|NCBI__GCF_000284315.1:WP_014449375.1 419 IKISSPTDFHQISGSVFQKRDYRIVSMDQLPVEVIPEPIMIYLTNQDQPGVVGAVGTILGNHKINISRM 487
                                               ********************************************************************* PP

                                 TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklve 524
                                               q gr+  gg+a+ ++ +D+e+s+ +l+e++++p+i s+k+++
  lcl|NCBI__GCF_000284315.1:WP_014449375.1 488 QFGRDYPGGKAISMIGVDNEISPALLSELRKIPNILSLKILH 529
                                               ************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (535 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.12
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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