GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Pseudomonas simiae WCS417

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate GFF4500 PS417_23035 PTS mannose transporter subunit IIC

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__WCS417:GFF4500
          Length = 838

 Score =  661 bits (1706), Expect = 0.0
 Identities = 391/844 (46%), Positives = 520/844 (61%), Gaps = 36/844 (4%)

Query: 6   LALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHALSL 65
           L L APLSG ++ L++VPDPVFSS  +G+G+ IDP +  L AP AG++S++  + HA+S+
Sbjct: 7   LELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSI 66

Query: 66  RADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITVMI 125
             DNG ++L+H+GLDTV L G+GF  LV+EG RV  GQPL+ FD D VA  +RSL+T+M+
Sbjct: 67  TDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLML 126

Query: 126 LTNGDGFQVRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHHGG 185
           + +G+ F +  L    VE G PLLQLSP  A +     A  E            + +  G
Sbjct: 127 VVSGEPFSL--LADGLVETGQPLLQLSPSGAVE-----AVDEEEGDALFSKPLTLPNANG 179

Query: 186 LHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSEAA 245
           LHARPAA+  + A+GF++   LH   Q A+  SLV IM L   + D ++V   GED+EAA
Sbjct: 180 LHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAA 239

Query: 246 LGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLAGVCASPGLASGPLARLGAISL 305
           + AL+A LA     A       +   EP    + A  L GVCASPG A G + ++    L
Sbjct: 240 IKALVALLAEGCGEA------VVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPEL 293

Query: 306 P-ADDGRHRPEEQH------LALDQALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALL 358
              + G     E+       LA ++ALQ ++D   GS Q          A IF AH  LL
Sbjct: 294 VITEQGTGGATERAALTRGLLAANEALQVLQDKAAGSAQ----------AEIFRAHQELL 343

Query: 359 EDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVLRVL 418
           EDP LL+ A  L+ +G  AA AW+ A  A   + Q LGN L+AERA DL D+ +RVL+++
Sbjct: 344 EDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLI 403

Query: 419 LG-DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCL 477
           LG   +   +P  AI+ A ++TPS  A L      G     GGATSHVAILAR+ GLP +
Sbjct: 404 LGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAI 463

Query: 478 VALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQ--ADAQRE 535
             + A +L L  G+QV+LDA +G L L P+   +EQ  L+ A++ +  R Q+  A A   
Sbjct: 464 CGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQ--LEAARKHQVLRHQRDVAQASLP 521

Query: 536 ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEV 595
           A TRDG  +E+ ANVAS +E   A   G +GVGLLR+EFL+L+R  AP  EEQ   Y  +
Sbjct: 522 ATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAI 581

Query: 596 LDAMG-QRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRALLR 654
             A+G +R +++RT+DVGGDK L Y+P+  E NP LGLRGI L   RP+LL +Q RA+L 
Sbjct: 582 ARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILA 641

Query: 655 VEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLAE 714
                R  I+LPMVS + EL   R+ L E A  LG+  LP+LG+MIEVPSAAL+AD  A 
Sbjct: 642 SAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAP 701

Query: 715 HADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGA 774
           H DF SIGTNDL+QY LAMDR H  LA++ D+ HPA+LRLIA T   A  HG+WVGVCGA
Sbjct: 702 HVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGA 761

Query: 775 LASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAVRDA 834
           LAS+ LA PVL+GLGV+ELSV   L+  IK  VR+LD A+C+  A+ +L L  A  VR+A
Sbjct: 762 LASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREA 821

Query: 835 CLQH 838
             Q+
Sbjct: 822 LRQY 825


Lambda     K      H
   0.319    0.136    0.390 

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: 1626
Number of extensions: 72
Number of successful extensions: 8
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: 842
Length of database: 838
Length adjustment: 42
Effective length of query: 800
Effective length of database: 796
Effective search space:   636800
Effective search space used:   636800
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 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