GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Lactobacillus silagei IWT126

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_089136332.1 CES79_RS03595 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo5_N2C3_1:AO356_17540
         (837 letters)



>NCBI__GCF_002217945.1:WP_089136332.1
          Length = 573

 Score =  311 bits (798), Expect = 5e-89
 Identities = 181/514 (35%), Positives = 286/514 (55%), Gaps = 11/514 (2%)

Query: 315 RLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSA-AP 373
           R+  AL+    ++    ++A+     D  AIF AH+A+L DP ++   D  I      A 
Sbjct: 43  RVHQALSVSVEDLKAIQDNAKGSLDEDTLAIFDAHIAILSDPEMIKQIDQEINDKKVNAE 102

Query: 374 HAWSR-SIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVLLGEAWQFDVAA---GAIVA 429
            A ++ + D    +     +  + ERA D++D+ +RVL  LLG+    D+AA     I+ 
Sbjct: 103 QALTKVTTDFANTLAAMTDNQYMQERAADVKDVSKRVLSHLLGKKLP-DLAAIDSPVIIV 161

Query: 430 AQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVV 489
           A E+TPSD  Q++ + + G+    GG TSH AI++R  G+P +V  G+     + G+ V+
Sbjct: 162 AHEVTPSDTSQMNKKFIKGMITDLGGRTSHSAIMSRTLGIPAVVGAGEATQKIKNGEVVI 221

Query: 490 LDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSA 549
           LD   G     P        +Q        RA+   L   P+ + DG E E+A+N+ + A
Sbjct: 222 LDGLNGEAISNPNETETKHYQQLAQSFEQQRAEWAKLVDAPSISADGKEFEIASNIGTPA 281

Query: 550 EAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGD 609
           +  + +  G+D VGL RTEFL++D  + P E++Q +AY+ V EAM  KPV+IRT+D+GGD
Sbjct: 282 DMDDVVKVGSDAVGLFRTEFLYMDSSSLPTEDDQFEAYKQVTEAMNGKPVVIRTMDIGGD 341

Query: 610 KQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPMVTEVDEL 669
           K L+YLPLP E NP LG R IR++  R  +   QLRAL++     + RI+ PM+  +DE 
Sbjct: 342 KPLNYLPLPEEMNPFLGYRAIRISLDRQSIFRTQLRALIRASKFGQLRIMFPMIATLDEF 401

Query: 670 -----LHIRKRLDALGSELGLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQY 724
                +   ++      + G+ +  +LG+M+E+PAAA+ AE  A+  DF SIGTNDL QY
Sbjct: 402 RKAKAIFTEEKKKLQVDDPGIGDDIKLGIMIEIPAAAIFAEAFAKEVDFFSIGTNDLIQY 461

Query: 725 TLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLG 784
           + A DR +  ++      +PALL+LI      A + G+   +CG +A D +A P+L+G+G
Sbjct: 462 SFAADRGNESVSYLYQPYNPALLKLIKHVIDAAHQEGKIAAMCGEMAGDAVALPLLMGMG 521

Query: 785 VRELSVSPPQIGEIKDRVRHLDAAQCARLSNELL 818
           + E S+S   +   +  ++ L+  +CA L N +L
Sbjct: 522 LDEYSMSSSSVLRTRSTMKTLNTEKCAELVNHVL 555


Lambda     K      H
   0.319    0.134    0.386 

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: 851
Number of extensions: 27
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: 837
Length of database: 573
Length adjustment: 39
Effective length of query: 798
Effective length of database: 534
Effective search space:   426132
Effective search space used:   426132
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: 54 (25.4 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:

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:

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:

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:

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