Alignments for a candidate for hpcD in Novosphingobium fuchskuhlense FNE08-7

GapMind for catabolism of small carbon sources

Alignments for a candidate for hpcD in Novosphingobium fuchskuhlense FNE08-7

Align propionyl-CoA synthase subunit (EC 1.3.1.84; EC 4.2.1.116; EC 6.2.1.36) (characterized)
to candidate WP_156424957.1 AQZ52_RS13685 AMP-binding protein

Query= metacyc::MONOMER-13612
         (1822 letters)



>NCBI__GCF_001519075.1:WP_156424957.1
          Length = 1804

 Score = 2150 bits (5571), Expect = 0.0
 Identities = 1101/1821 (60%), Positives = 1347/1821 (73%), Gaps = 63/1821 (3%)

Query: 28   RAAALADPGAFHGAIARTVIHWYDPQ---HHCWIRFNESSQRWEGLDAATGAPVTVDYPA 84
            RAAAL DPGAFHG IA   IHW+         W+  +E+   W G DAATG  VT D PA
Sbjct: 2    RAAALTDPGAFHGDIAARRIHWFVASCGPDGAWLTRDEAGA-WTGWDAATGVTVTPDLPA 60

Query: 85   DYQPWQQAFDDSEAPFYRWFSGGLTNACFNEVDRHVMMGYGDEVAYYFEGDRWDNSLNNG 144
             + PW +AFDDS  P +RWF+G  TNA FNE+DRHV+ G+G E A  FEGDRWD + + G
Sbjct: 61   SFAPWTKAFDDSTPPHWRWFTGARTNAAFNEIDRHVLSGHGAEAALIFEGDRWDMAADGG 120

Query: 145  RGGPVVQETITRRRLLVEVVKAAQVLRDLGLKKGDRIALNMPNIMPQIYYTEAAKRLGIL 204
            RG PV   T++R+RLL+EV K A  L  LGLK GDRIALNMP+I+PQI++TEAAKRLGI+
Sbjct: 121  RGAPVDTFTVSRKRLLLEVAKCAVALESLGLKAGDRIALNMPSIVPQIFWTEAAKRLGIV 180

Query: 205  YTPVFGGFSDKTLSDRIHNAGARVVITSDGAYRNAQVVPYKEAYTDQALDKYIPVETAQA 264
            YT VFGGFSDKTLSDRI +AGARV++TSDG+YRNAQV  +K AYTD ALD Y+PV TA +
Sbjct: 181  YTAVFGGFSDKTLSDRIADAGARVIVTSDGSYRNAQVAAFKTAYTDPALDNYVPVSTALS 240

Query: 265  IVAQTLATLPLTESQRQTIITEVEA-ALAGEITVERSDVMRGVGSALAKLRD---LDASV 320
            ++A T   LP  ++    +IT+  A  LAGE+TVERSDVMRGVG AL +L +   + AS 
Sbjct: 241  VLAATDFGLPAEDA---AVITDTVAETLAGEVTVERSDVMRGVGRALIRLGETGRIGASD 297

Query: 321  QAKVRTVLAQALVESPPRVEAVVVVRHTGQ-EILWNEGRDRWSHDLLDAALAKILANARA 379
             A+VR  +A +LV  PPRV+ V+VVRHT Q +I+W   RDRWSH+L DAAL  IL  A  
Sbjct: 298  AARVRLAIASSLVTLPPRVDTVIVVRHTAQPDIVWRTERDRWSHELTDAALETILQKAGV 357

Query: 380  AGFDVHSENDLLNLPDDQLIRALYASIPCEPVDAEYPMFIIYTSGSTGKPKGVIHVHGGY 439
            A     SE+ LL LPD   +RA++AS    PVD+EYP+F IYTSGSTGKPKG++HVHGGY
Sbjct: 358  A-----SEDALLALPDADFVRAIWASSKPLPVDSEYPLFFIYTSGSTGKPKGIVHVHGGY 412

Query: 440  VAGVVHTLRVSFDAEPGDTIYVIADPGWITGQSYMLTATMAGRLTGVIAEGSPLFPSAGR 499
             AG+ H+++V+FDA PGDTI+V+ADPGWITGQSY ++A++  R+T V++EGSP+FP AGR
Sbjct: 413  TAGIAHSMQVAFDARPGDTIFVVADPGWITGQSYQISASLLSRVTTVVSEGSPVFPHAGR 472

Query: 500  YASIIERYGVQIFKAGVTFLKTVMSNPQNVEDVRLYDMHSLRVATFCAEPVSPAVQQFGM 559
            +AS+IER+ V IFKAGVTFLK++MS+P N+ DV+ YDM  LRVATFCAEP SP+VQ FGM
Sbjct: 473  FASMIERHKVTIFKAGVTFLKSIMSDPSNLADVQRYDMSHLRVATFCAEPTSPSVQAFGM 532

Query: 560  QIMTPQYINSYWATEHGGIVWTHFYGNQDFPLRPDAHTYPLPWVMGDVWV----AETDES 615
            + +T QYINSYWATEHGGI WTHFYGN DFPL+ DAH +PLPW++GDVWV    A   +S
Sbjct: 533  EHVTRQYINSYWATEHGGIAWTHFYGNADFPLKADAHAFPLPWIVGDVWVEDEAATPGKS 592

Query: 616  GTTR-------YRVADFDEKGEIVITAPYPYLTRTLWGDVPGF---EAYLRGEIPLRAWK 665
              TR       +R A+  EKGEIVI APYPYL RT+WGDV  F   +  ++G+     WK
Sbjct: 593  PFTRAGTEGVTWRRAEPGEKGEIVIAAPYPYLARTIWGDVENFRVKDGSVQGD-----WK 647

Query: 666  GDAERFVKTYWRRGPNGEWGYIQGDFAIKYPDGSFTLHGRSDDVINVSGHRMGTEEIEGA 725
            GDA R+   YW R   G W Y QGDFAI +PDGSF+ HGRSDDVINVSGHRMGTEEIEGA
Sbjct: 648  GDAGRWESGYWSRW-QGAWAYTQGDFAIAHPDGSFSFHGRSDDVINVSGHRMGTEEIEGA 706

Query: 726  ILRDRQITPDSPVGNCIVVGAPHREKGLTPVAFIQPAPGRHLTGADRRRLDELVRTEKGA 785
            +LRD+ + P+SPVGN +VVGAPHREKGLTP+AF+ P  GR LT  DR+RL  LVRTEKGA
Sbjct: 707  VLRDKALDPNSPVGNVLVVGAPHREKGLTPLAFVVPVAGRKLTEEDRQRLFNLVRTEKGA 766

Query: 786  VSVPEDYIEVSAFPETRSGKYMRRFLRNMMLDEPLGDTTTLRNPEVLEEIAAKIAEWKRR 845
            V+VP D+IEVS FPETRSGKYMRR +R ++    LGD TTLRNPE L E+   I  W+R+
Sbjct: 767  VAVPADFIEVSQFPETRSGKYMRRMVRALVEGGDLGDVTTLRNPESLTELKTAIDAWQRQ 826

Query: 846  QRMAEEQQIIERYRYFRIEYHPPTASAGK-LAVVTVTNPPVNALNERALDELNTIVDHLA 904
            QR++EEQ + ERYRYF I+Y+  T + GK +A VTVTNPPVNALNERA+DEL  +V+HL+
Sbjct: 827  QRLSEEQSLFERYRYFLIQYN--TVAPGKRVATVTVTNPPVNALNERAIDELVIVVEHLS 884

Query: 905  RRQDVAAIVFTGQGARSFVAGADIRQLLEEIHTVEEAMALPNNAHLAFRKIERMNKPCIA 964
            R+ DV A+VFTG+G  SFVAGADIRQ+LEEIH+ +EA+ LPNNA LAFRKIE M KPCIA
Sbjct: 885  RKDDVVAVVFTGEGTSSFVAGADIRQMLEEIHSHDEALVLPNNAQLAFRKIELMGKPCIA 944

Query: 965  AINGVALGGGLEFAMACHYRVADVYAEFGQPEINLRLLPGYGGTQRLPRLLYKRNNGTGL 1024
            A+ GVALGGG+EFA+ACH RVA+  A FGQPEI LRLLPGYGGTQRLPRLL  R+  TG+
Sbjct: 945  AVQGVALGGGMEFALACHVRVAETTARFGQPEIRLRLLPGYGGTQRLPRLLADRHGATGV 1004

Query: 1025 LRALEMILGGRSVPADEALELGLIDAIATGDQDSLSLACALARAAI--GADGQLIESAAV 1082
              AL++ILGGRS+ A +A  +GL+DA+A G +D+L+ A A+ R  +  GA+  L      
Sbjct: 1005 RDALDLILGGRSIDAAQAQAIGLVDALADGHRDALAEAHAMVRDWVKRGAESPL------ 1058

Query: 1083 TQAFRHRHEQLDEWRKPDPRFADDELRSIIAHPRIERIIRQAHTVGRDAAVHRALDAIRY 1142
             +AF  R E    W KP    +  +L S++    ++RI+RQ    GR  A  RALDA+R 
Sbjct: 1059 GKAFAAREEATVLWDKP----STVDLDSVLQDDFLQRILRQLDWAGRGQAGTRALDAVRT 1114

Query: 1143 GIIHGFEAGLEHEAKLFAEAVVDPNGGKRGIREFLDRQSAPLPTRRPLITPEQEQLLRDQ 1202
            G+  G  AGL  EA LFAEA++DP GGK GIR+F+D+ + PLP RR  +  + E   R  
Sbjct: 1115 GLADGISAGLAREAALFAEAIIDPEGGKTGIRQFMDKVAPPLPVRRDGVWIDSEHETRAA 1174

Query: 1203 K-----ELLPVGSPFFPGVDRIPKWQYAQTVIRDPDTGAAAHGDPIVAEKQIIVPVERPR 1257
            +     +LLPVG+PF+PGV  IP +QYA  + RDPDTGA   G P   E+++IV V  P 
Sbjct: 1175 ELEANGDLLPVGAPFYPGVTAIPPYQYAFGIARDPDTGAPRFGPPATHERELIVKVPEPA 1234

Query: 1258 ANQALIYVLASEVNFNDIWAITGIPVSRFDEHDRDWHVTGSGGIGLIVALGEEARREGRL 1317
             N+AL+Y+L SEVNFNDIWA+TGIPVS FD H+ D  +TGSGGI L+ ALG E R EGR+
Sbjct: 1235 PNEALLYMLTSEVNFNDIWALTGIPVSPFDSHEEDVQITGSGGIALVAALGSETRSEGRI 1294

Query: 1318 KVGDLVAIYSGQSDLLSPLMGLDPMAADFVIQGNDTPDGSHQQFMLAQAPQCLPIPTDMS 1377
            KVGDLV +YSG +DLLSP +G DPM ADF IQG +T  GSH QF+  QAPQ   +P +++
Sbjct: 1295 KVGDLVTVYSGTNDLLSPAVGNDPMFADFSIQGYETETGSHAQFLTVQAPQMHKVPPNLT 1354

Query: 1378 IEAAGSYILNLGTIYRALFTTLQIKAGRTIFIEGAATGTGLDAARSAARNGLRVIGMVSS 1437
            +E AGSY+LNLGTI R LFTTLQI  GRT+F+EGAATGTGLDA RS+ R GL+V G+VSS
Sbjct: 1355 LEQAGSYVLNLGTISRCLFTTLQIAPGRTLFVEGAATGTGLDALRSSVRTGLQVTGLVSS 1414

Query: 1438 SSRASTLLAA-GAHGAINRKDPEVADCFTRVPEDPSAWAAWEAAGQPLLAMFRAQNDGRL 1496
              RA+ +    GA GAINRKDP  A  +T VPED +   AWEAAG PL+  ++A N G+L
Sbjct: 1415 PDRAAFITGQQGAVGAINRKDPRFAALYTTVPEDAAEARAWEAAGAPLVEEYKALNGGKL 1474

Query: 1497 ADYVVSHAGETAFPRSFQLLGEPRDGHIPTLTFYGATSGYHFTFLGKPGSASPTEMLRRA 1556
            ADYVVSHAGETAFPRSFQLL E       TL FYGA+SGYHF+F+GKPG+ASP EMLRRA
Sbjct: 1475 ADYVVSHAGETAFPRSFQLLAEGG-----TLAFYGASSGYHFSFMGKPGAASPEEMLRRA 1529

Query: 1557 NLRAGEAVLIYYGVGSDDLVDTGGLEAIEAARQMGARIVVVTVSDAQREFVLSLGFGAAL 1616
             LR GEAVLIYYG GSD L+D  GLE IEAAR+  AR VV T +D QREF+ SLG   A+
Sbjct: 1530 ALRGGEAVLIYYGPGSDALLDDMGLEIIEAARRFNARSVVATTTDGQREFLGSLGLEDAI 1589

Query: 1617 RGVVSLAELKRRFGDEFEWPRTMPPLPNARQDPQGLKEAVRRFNDLVFKPLGSAVGVFLR 1676
             G+VSL  ++RR GD F WP TMP LP+A+ D +  K AVR + D V KP GSA+G  LR
Sbjct: 1590 EGIVSLESIRRREGDNFLWPDTMPRLPDAKADIEVFKAAVRDYQDRVMKPFGSAIGKILR 1649

Query: 1677 SADNPRGYPDLIIERAAHDALAVSAMLIKPFTGRIVYFEDIGGRRYSFFAPQIWVRQRRI 1736
            SADNPRG PDL+ ER   D L VS  L+KPFTGR+V+ ED+ G R++F+APQ+W RQR+I
Sbjct: 1650 SADNPRGAPDLVFERTGQDTLGVSTSLVKPFTGRVVFAEDLTGSRFTFYAPQVWTRQRKI 1709

Query: 1737 YMPTAQIFGTHLSNAYEILRLNDEISAGLLTITEPAVVPWDELPEAHQAMWENRHTAATY 1796
             MPTA I GTHL NA+E+ R+ND I+A LL +TEP VV WD LPEAHQ+MW+NRH+ ATY
Sbjct: 1710 LMPTASILGTHLCNAFEVARMNDMIAASLLEVTEPEVVGWDGLPEAHQSMWDNRHSGATY 1769

Query: 1797 VVNHALPRLGLKNRDELYEAW 1817
            VVNHALP +GL++RD L EAW
Sbjct: 1770 VVNHALPAMGLRSRDALLEAW 1790


Lambda     K      H
   0.320    0.137    0.415 

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: 8348
Number of extensions: 405
Number of successful extensions: 16
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: 1822
Length of database: 1804
Length adjustment: 53
Effective length of query: 1769
Effective length of database: 1751
Effective search space:  3097519
Effective search space used:  3097519
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: 62 (28.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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

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 catabolism of small carbon sources