Alignments for a candidate for nagEIIA in Clostridium tyrobutyricum FAM22553

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagEIIA in Clostridium tyrobutyricum FAM22553

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate WP_039653499.1 PN53_RS12165 glucose PTS transporter subunit IIA

Query= SwissProt::P39816
         (631 letters)



>NCBI__GCF_000816635.1:WP_039653499.1
          Length = 667

 Score =  576 bits (1485), Expect = e-168
 Identities = 315/649 (48%), Positives = 421/649 (64%), Gaps = 38/649 (5%)

Query: 1   MFKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAV 60
           M KK F +LQ++G++LM PV+VLPAAG+LLR G  DLLN+P I+ AG  +F NLP+IFAV
Sbjct: 1   MKKKIFSVLQKIGKSLMLPVSVLPAAGILLRLGQPDLLNMPYIEAAGNAIFTNLPMIFAV 60

Query: 61  GVAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLG------LQPPYEGAEHL------- 107
           GVAIG +GGE VA LAAV+G LIL    +N+ KL        L      + H+       
Sbjct: 61  GVAIGFSGGEAVAALAAVVGELIL----ENIEKLASSNAATALAQTTAASHHMTLKAFME 116

Query: 108 ------------IDMGVFGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSS 155
                       I+MGVFGGIIIG++AA LY RF SI+L  VLGFF GKRFVPI+TS ++
Sbjct: 117 TQVYQNIVTKTTINMGVFGGIIIGIVAALLYNRFHSIKLPQVLGFFGGKRFVPIVTSAAA 176

Query: 156 LVIGVIFSFVWPLIQNGINAASSLIADSTVGLFFYATIYRLLIPFGLHHIFYTPFYFMMG 215
           L+IG I   +W  +Q  I+  ++L ++S +G  FYA   RLLIP GLHHI+Y  F +  G
Sbjct: 177 LIIGAIGVSIWVPVQGWIDTMANLASNSALGPAFYAAGKRLLIPVGLHHIYYPVFLYQFG 236

Query: 216 EYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMIS 275
            +   S G T  GD  R+F GDPTAG FM  +FP ++F LP  ALA+I  A+  K+K ++
Sbjct: 237 HFI--SNGITYIGDSPRYFHGDPTAGIFMASEFPILMFGLPGAALAMIAAAKKSKRKQMA 294

Query: 276 GVMISAALTSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGG 335
           G+MIS+A  + +TGITEP+EFSF+FVAP+L++ + ++A    +V    H+R GYTFS   
Sbjct: 295 GMMISSAFVAFVTGITEPIEFSFIFVAPILFVFHVLVAFCSGLVTSFLHIRLGYTFSASF 354

Query: 336 IDYVLNYGLSTNGWVVIPVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVA 395
           IDY+L +  + + W++ PVG+ F  +Y+ +F F I   NLKTPGRE DEDG+      V 
Sbjct: 355 IDYILGFRYAEHPWLIWPVGVAFFLLYFVVFYFLIRAMNLKTPGRE-DEDGEEIVHINVK 413

Query: 396 KDQLAFHVLQALGGQQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNNFQA 455
               A  VL+A+GG+ NI  LDACITRLR+T++ P+ V +  L+ LGA G+++  N+ Q 
Sbjct: 414 GSAKAAKVLEAIGGKDNIKVLDACITRLRLTLNDPA-VDEKTLRALGAAGIMKAGNSVQV 472

Query: 456 IFGTKSDALKDDIKTIMA-GGV---PATAAALDTVTDKPLKPDSD-ETFIYPIKGETVSL 510
           +FGT+++ +KDDIK I+A GGV     T    DT      K  S     + P  GE V+L
Sbjct: 473 VFGTEAERIKDDIKAIIANGGVVEESETQQGEDTSGGSESKAVSGVNLLLSPADGEIVTL 532

Query: 511 GDVPDQVFSEKMMGEGFAIIPSEGKVVAPADGEIVSIFPTKHAIGFMSAGGTEILIHVGI 570
            +VPD  FSEK++G+GFA+IPS   + APADGEI  +FPTKHA    +A G E+LIH+GI
Sbjct: 533 EEVPDPTFSEKLLGDGFAVIPSGDNIYAPADGEITVLFPTKHAFAITTAQGLELLIHIGI 592

Query: 571 DTVKLNGEGFEAHVTSGQAVKQGELLLTFDLNYIKQHAASAITPVIFTN 619
           DTV LNGEGF AHV  G  VK+G+L+L  D  +IK    + ITPVI TN
Sbjct: 593 DTVALNGEGFTAHVKQGDKVKKGDLILNLDSKFIKSKGKNMITPVIVTN 641


Lambda     K      H
   0.324    0.142    0.421 

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: 1087
Number of extensions: 47
Number of successful extensions: 7
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: 631
Length of database: 667
Length adjustment: 38
Effective length of query: 593
Effective length of database: 629
Effective search space:   372997
Effective search space used:   372997
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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