Alignments for a candidate for serA in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Alicycliphilus denitrificans K601

Align Phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_013721498.1 ALIDE2_RS04555 FAD-linked oxidase

Query= reanno::BFirm:BPHYT_RS03150
         (1364 letters)



>NCBI__GCF_000204645.1:WP_013721498.1
          Length = 1305

 Score = 1771 bits (4587), Expect = 0.0
 Identities = 906/1395 (64%), Positives = 1057/1395 (75%), Gaps = 121/1395 (8%)

Query: 1    MNAPQVFDPHGAAATVAADPEARLREIPYNYTSFSDREIVIRLLGDEAWAVLAELRAERR 60
            MNAP       AA         RLREIPYNYTSFSDREIVIRLLG +AW VL  LR ERR
Sbjct: 1    MNAPIAL----AALQAQGSEPVRLREIPYNYTSFSDREIVIRLLGAQAWDVLDHLRRERR 56

Query: 61   TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAMLIEALHHRLSEIEKRRRADLTEH 120
            TGRSARMLYEVLGDIW V+RNPYLQDDL+ NP+RR ML++A+ HR+ EIEKRR       
Sbjct: 57   TGRSARMLYEVLGDIWAVQRNPYLQDDLIHNPQRRKMLVDAMRHRMGEIEKRRTP----- 111

Query: 121  GDEAGVDRAARVETLVQAARRAVDEFASEFQKTYDLRKRATKVLGKVTEKDNIKFDGLSR 180
              +   +R  RV  LV+AA RA+ EF +   +   +RK   + L + T KDNIKFDGLSR
Sbjct: 112  --QEDPERDRRVAQLVEAANRAIAEFDATLVEVAGMRKLVARRLARHTAKDNIKFDGLSR 169

Query: 181  VSHVTDATDWRVEYPFVVLTPDTEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF 240
            VSHVTDATDWRVE+PFVVLTPDTE E A ++K C EL LT+IPRGGGTGYTGGA+PL+  
Sbjct: 170  VSHVTDATDWRVEFPFVVLTPDTEGETAALVKECIELDLTIIPRGGGTGYTGGAIPLSWR 229

Query: 241  SAVINTEKLEQLGAVEMTELPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD 300
            SAVINTEKLE +  VEM  LPG+   V T+++ AGVVT+RV +AAE+ G+VFAVDPTS++
Sbjct: 230  SAVINTEKLEAMTEVEMVRLPGLAHDVPTVWTEAGVVTQRVADAAERGGYVFAVDPTSIE 289

Query: 301  ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNMGKIHDIEVARF 360
            ASC+GGN+AMNAGGKKAVLWGTALDNLA WRMV P+  WLEVTR++HN+GKIHD EVA F
Sbjct: 290  ASCIGGNIAMNAGGKKAVLWGTALDNLASWRMVTPQAQWLEVTRINHNLGKIHDAEVASF 349

Query: 361  RLDWFDGNYAPGEKLMRTEALDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA 420
             L +F+   A G   +RTE LDI G+ FRKEGLGKDVTDKFL+GLPGVQKEG DGLITSA
Sbjct: 350  ELAYFE---ADGRTPVRTERLDIPGKSFRKEGLGKDVTDKFLSGLPGVQKEGTDGLITSA 406

Query: 421  RWVLHKMPAHTRTVCLEFFGQARDAIPSIVEIKDYLFETSKQGGAILAGLEHLDERYLRA 480
            RW++H+MPAHTRTVCLEFFG A++A+PSIVEIKD++F   K+ G +LAGLEHLD+RYL+A
Sbjct: 407  RWIVHRMPAHTRTVCLEFFGSAKEAVPSIVEIKDFMFAEQKRSGVLLAGLEHLDDRYLKA 466

Query: 481  VGYATKSKRNA--FPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVNAEARKR 538
            VGYATKSK+     PKMVLIGD+VGDDADAVA+AT+EVVR+AN +SGEGF AV++EARK+
Sbjct: 467  VGYATKSKKGGGRLPKMVLIGDLVGDDADAVARATAEVVRIANSRSGEGFTAVSSEARKQ 526

Query: 539  FWLDRSRTAAIAKHTNAFKINEDVVIPLDRMGEYTDGIERINIELSIKNKLQLVDALEAF 598
            FWLDR RTAAI++HTNAFKINEDVVIPL RM EYTDGIERINIELS++NKL+L DAL+ F
Sbjct: 527  FWLDRKRTAAISRHTNAFKINEDVVIPLPRMAEYTDGIERINIELSLRNKLKLCDALQDF 586

Query: 599  FKGGKLPLGKSDDANEIPSAELLEDRVQQALDLLKRVRTRWEFLRDKLDLSLREAQHYLV 658
            F    LP  K  DA  +P AELL DRV QA  L+  VR  W+   D +            
Sbjct: 587  FARPDLPCAKQGDA--LPDAELLGDRVAQAQALVAEVRALWQGWLDDV------------ 632

Query: 659  GLGYEAMAEKFADRVDAQPDVNVFHVTQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEA 718
                                  +F   QD ++R SWK ++R  L +IF G  F+P++ EA
Sbjct: 633  --------------------ARLFPQLQDHSLRASWKTQLRQPLAEIFVGAAFEPLMQEA 672

Query: 719  QAIHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHTAVARIMKLARSLDGVI 778
             AIHKQVL+GRV+VALHMHAGDGNVHTN+PVNSD+YEMLQ AH AV RIM+LARSLDGVI
Sbjct: 673  AAIHKQVLKGRVWVALHMHAGDGNVHTNIPVNSDDYEMLQTAHEAVGRIMQLARSLDGVI 732

Query: 779  SGEHGIGITKLEFLTEDEISEFRQYKQRVDPHGRFNAGKLLEG----------------- 821
            SGEHGIGITKLEFL+++E++ F  YK+R+DP G FN GKLL                   
Sbjct: 733  SGEHGIGITKLEFLSDEELAPFADYKRRIDPQGHFNRGKLLRNQELQGQVYQALEANSAH 792

Query: 822  ---------ADLRNAYTPSFGLMGYESLIMQQSDIGAISESIKDCLRCGKCKPVCATHVP 872
                     ADL NAYTPSFGLMGYESLIMQQSDIG I  S+KDCLRCGKCKPVC+THVP
Sbjct: 793  NGPRRSLPFADLTNAYTPSFGLMGYESLIMQQSDIGQIVASVKDCLRCGKCKPVCSTHVP 852

Query: 873  RANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWDEFNDVADHCTVCHKCVTPCPVK 932
            RANLLYSPRNKILATSLL EAFLYEEQTRRG+S  HW EF DVADHCT+CH+C  PCPVK
Sbjct: 853  RANLLYSPRNKILATSLLAEAFLYEEQTRRGISSHHWQEFEDVADHCTICHRCYNPCPVK 912

Query: 933  IDFGDVTMNMRNLLRKMGKKKFNPGNAAGMFFLNATNPQTINLARTAMMGVGYKAQRLGN 992
            IDFGDVTM MR+LL KM KK + PGN   M  LNAT+P+TINL R  M+ VG+KAQRL  
Sbjct: 913  IDFGDVTMAMRSLLVKMNKKSWRPGNKLAMAMLNATDPRTINLLRAGMVNVGFKAQRLAV 972

Query: 993  EVLKKFTKKQTAHPPATVGKPPVTQQVIHFMNKKMPGNLPKKTARALLDIEDNKIVPIIR 1052
            + L+  +K QTA PPATVG  P+ +QVIHF+NKK+PG LP +TARALLDIE+   VPIIR
Sbjct: 973  DALRSVSKAQTARPPATVGTAPIKEQVIHFVNKKLPGGLPTRTARALLDIENKDYVPIIR 1032

Query: 1053 NPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQ 1112
            +P+ T+AD+EAVFYFPGCGSERLFSQVGLATQAMLW AGVQTVLPPGYLCCGYPQRG+G 
Sbjct: 1033 DPQ-TSADSEAVFYFPGCGSERLFSQVGLATQAMLWHAGVQTVLPPGYLCCGYPQRGNGL 1091

Query: 1113 FDKAEQIVTDNRVLFHRVANTLNYLDIKTVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHE 1172
             DKAE+++TDNRVLFHRVANTLNYLDIKTVVVSCGTCYDQL GYEF+KIFPG RIIDIHE
Sbjct: 1092 QDKAEKMITDNRVLFHRVANTLNYLDIKTVVVSCGTCYDQLQGYEFDKIFPGSRIIDIHE 1151

Query: 1173 FLLEKGMKLDGVNGVRYMYHDPCHTPIKTMDPIKLVNQLMGSEKDGYKIEKNDRCCGESG 1232
            +LLEKG+ L    G  Y+YH+PCH P+K  D +K V  L+G      K+ K+DRCCGESG
Sbjct: 1152 YLLEKGITLPAGQG--YLYHEPCHNPMKLGDSMKTVRALVGD-----KVLKSDRCCGESG 1204

Query: 1233 TLAVTRPDISTQVRFRKEEEIRKGAAKLRGIPLVAEAGANGINPANASAGSAGAPEGSVL 1292
            TL V+RPD+STQVRFRK EEIRKG A+LRG                  +G+ GA +    
Sbjct: 1205 TLGVSRPDVSTQVRFRKTEEIRKGEAQLRG------------------SGAVGATD---- 1242

Query: 1293 KAGDGPQPKGATDVKILTSCPSCLQGLSRYNEDAG---IEADYIVVEMARHVLGEDWMVD 1349
                        ++KILTSCPSCLQG+SRY +D     +EADYIV+EMAR +LGE+W+ +
Sbjct: 1243 ------------NIKILTSCPSCLQGISRYQDDLQTGLLEADYIVIEMARQILGENWLPE 1290

Query: 1350 YVQRANNGGIERVLV 1364
            YVQRAN GGIERVLV
Sbjct: 1291 YVQRANAGGIERVLV 1305


Lambda     K      H
   0.320    0.136    0.406 

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: 4186
Number of extensions: 153
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1364
Length of database: 1305
Length adjustment: 49
Effective length of query: 1315
Effective length of database: 1256
Effective search space:  1651640
Effective search space used:  1651640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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