Alignments for a candidate for nagF in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Oceanisphaera arctica V1-41

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_104485039.1 UN63_RS01625 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>NCBI__GCF_002936955.1:WP_104485039.1
          Length = 949

 Score =  450 bits (1158), Expect = e-130
 Identities = 296/719 (41%), Positives = 394/719 (54%), Gaps = 29/719 (4%)

Query: 145 LKAGETPLLVLRARDGAAAEASRQLSSTNVTEEA--------------RQQVTLVHAGGL 190
           ++  E   L+ R  D  AA    +L+  +  E                ++ V + +  GL
Sbjct: 236 VRGSEHKTLLTRVADWLAAGRGAELAGQDSAEALLNVLKRGPVSLSSHQRTVVVRNTHGL 295

Query: 191 HARPAARAREAARGFDARVEV-RYEGRK--AAIESVVGLLGLGAGEGATVELLGMGPQAA 247
           HARP A   +AA+ FDA ++V   +G +   + +S++ ++GLG   G  +     GP A 
Sbjct: 296 HARPGAMLVQAAKNFDADIQVCNLDGDEHWVSAKSLMKMIGLGVKAGHQLVFRAEGPDAE 355

Query: 248 AAVAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAPNTLA-GVCAAPGVAVGK 306
           AA+ A+  E      GE     A +       +  P G  + PNTL  GV A+PG+A+G 
Sbjct: 356 AALDALT-EAVNGGLGEAFVAQATEPQAEEHDIHEPQG--IDPNTLVRGVAASPGIAIGP 412

Query: 307 LVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHR 366
           +        D P++A G + AE + L  AI    A+L  T+R  S   A     + S+HR
Sbjct: 413 VFVDAPLRFDYPQQA-GDTQAEQQKLSAAIEQASAELSATLRRLSDTQA---RDMMSMHR 468

Query: 367 VLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVL 426
            LL D +L       I  G+SA  AW   I +         DALLAERAAD+RDI +RV+
Sbjct: 469 ELLADSSLTQGVSCRIKQGQSAAAAWWSEIDSAADRQAASSDALLAERAADIRDIGRRVM 528

Query: 427 RALGYTSATARTLPEEAVL-AAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAG 485
             L ++  T    PE   L  A++  PS L  LD SRV  LV   GGA+SH+AILAR  G
Sbjct: 529 AILCHSRMTPP--PEHPYLWLAQDIGPSQLVNLDPSRVLGLVTVGGGASSHSAILARSLG 586

Query: 486 IPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQ 545
           IPALVA G A+ A+P GT+ ++N   G L  AP    +E+AR+ + R  +  E +     
Sbjct: 587 IPALVAAGGAVMALPSGTEAILNGDDGTLWVAPEAAMLEQARVRQQREREQAEQDWMRRH 646

Query: 546 QAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQ 605
            AA+T DG  I VAAN+A    A+  +E GA+ VGLLRTE +F+ R + P  DE    Y+
Sbjct: 647 DAAITLDGHRIGVAANLADTGQAREVMEVGAEGVGLLRTEFVFMARHSEPDLDEQLAFYR 706

Query: 606 AIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLL 665
              DAL GR  + RTLDVG DK + Y  +P E NP LG+RGIRL   +P+LL  QLR LL
Sbjct: 707 QAFDALDGRPLVARTLDVGGDKPLPYWPVPKEDNPFLGVRGIRLCMQKPELLKTQLRALL 766

Query: 666 AVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLA 725
                  +RI+ PMV D  E    +   D+   E+  T+ ++VG+M+EVPS AL A   A
Sbjct: 767 MAAGDRPLRIMFPMVADWSEWRWAKALFDKIQSEVQATD-VQVGIMVEVPSVALNAAVFA 825

Query: 726 QHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCG 785
           +  DF SIGTNDLTQYTLAMDR    LA  +DGL+PAVLRLI   V  A   GKWVGVCG
Sbjct: 826 EEVDFFSIGTNDLTQYTLAMDRGNGGLARLSDGLNPAVLRLIKMVVDAAHAKGKWVGVCG 885

Query: 786 ALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVR 844
            LA DP+A+PLL+GLGV ELSV    V  +KA+VR      CR+ A+ AL    A AVR
Sbjct: 886 ELASDPVALPLLLGLGVDELSVSLKRVTLVKAQVREWSLSSCRKLAEQALQAVDAPAVR 944


Lambda     K      H
   0.317    0.133    0.371 

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: 1590
Number of extensions: 73
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: 854
Length of database: 949
Length adjustment: 43
Effective length of query: 811
Effective length of database: 906
Effective search space:   734766
Effective search space used:   734766
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 (21.7 bits)
S2: 56 (26.2 bits)

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

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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

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