Alignments for a candidate for fruII-ABC in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Photobacterium jeanii R-40508

Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate WP_068334611.1 A3K86_RS18075 PTS transporter subunit EIIA

Query= TCDB::P71012
         (635 letters)



>NCBI__GCF_001650345.1:WP_068334611.1
          Length = 646

 Score =  429 bits (1103), Expect = e-124
 Identities = 257/653 (39%), Positives = 384/653 (58%), Gaps = 44/653 (6%)

Query: 3   ITELLTKHTIKLNIESKEKENVIDEMVTVLDKAGKLNDRQAYKEAILNRESQSSTGIGEG 62
           IT L+ +  IKL++++  KE V +E++ +L   G+++D+  +   I  RE+  +TG  EG
Sbjct: 2   ITTLINQDLIKLDLQADSKEAVFNELIEILFAQGRISDKAQFLADIQAREAVGNTGFEEG 61

Query: 63  IAIPHAKTASVINPAIAFGRSKDGVDYESLDGQPAHLVFMIAATEGANNTHLEALSRLST 122
           +AIPHAK+A+V+ PA+  G S+ G+DY + DG P+ L FMIA+ +G +N H+E L++LS+
Sbjct: 62  VAIPHAKSAAVLKPAVVIGVSQSGIDYGAEDGLPSKLFFMIASPDGGDNHHIEVLAQLSS 121

Query: 123 LLMREEIRKQLLEAESEDAIIDIINQHDKDDDEEEEEEEAAPAP------AGKGKILAVT 176
            L+ +      + A S +A + ++           E+ +AAP+       A +G I+ VT
Sbjct: 122 KLIEDGFIDNFINAPSNEAALALL---------LAEQNQAAPSTPSHTDVANQGFIIGVT 172

Query: 177 ACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQV 236
            CP G+AHT++AA+AL++ A ELG +I VETNGS G+K+  +A +I  A AI+VA DKQV
Sbjct: 173 GCPAGVAHTYLAAEALQKGATELGYDILVETNGSIGVKNSPSADDIARADAIVVACDKQV 232

Query: 237 EMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAK--GKSG 294
           +M RF GKR+++  V A I+  + +I +A+   AP YQ   G + AS     A       
Sbjct: 233 DMTRFAGKRLIKTNVKAPIKDAKGVINQAL--AAPQYQVEQGANPASQAATSANSMASKA 290

Query: 295 SGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSAD-----PNDPSYNTFAAALN 349
           S   +  Y++LM+GVS+M+PFVV GG+L+A++   G   ++     P    +N       
Sbjct: 291 SDARSDLYRYLMNGVSHMIPFVVTGGLLIALALAIGGEPSEAGMAIPKGSMWNQILDV-- 348

Query: 350 FIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMA-------TQANAGFLGGLIAG 402
              G  A  L++ +LAG+IA +IADRP  APG++GG++A         A  GF+G ++AG
Sbjct: 349 ---GVVAFTLMIPILAGYIAYAIADRPALAPGLIGGWIANNGSFYGADAGTGFIGAIVAG 405

Query: 403 FLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFG-IFITGVLMQFVVNTPVAAFMNFLTN 461
            L GY V  +  V     + +  L P++I P+ G +FI G+ + FV+  P+A  M  LT 
Sbjct: 406 LLVGYFVKWI--VSINYHKFIQPLVPIMIAPITGSLFIAGLFI-FVIGAPIADLMTSLTA 462

Query: 462 WLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPP 521
            L S+ TGN++L+GI+LGGM   DMGGP NK AF F + MI +G      A+     V P
Sbjct: 463 LLTSMSTGNVILLGIVLGGMAGFDMGGPFNKVAFLFSVGMIASGQTQFMGAMACAIPVAP 522

Query: 522 LGIALATTIFR--NKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAV 579
           LG+ALAT + R    F   + EAG     MG   ++EGAIPFAA DP+ VIPA V+G+ V
Sbjct: 523 LGMALATALGRKFELFEASELEAGKAAGAMGLVGISEGAIPFAAQDPMSVIPANVLGSMV 582

Query: 580 AGGLTEFFRVTLPAPHGGVFVAFI--TNHPMLYLLSIVIGAVVMAIILGIVKK 630
           A  +   F +T    HGG  VA +   NHP+L L+ +  GA V A+    +KK
Sbjct: 583 AAVMAFSFGITNSVAHGGPVVALLGAMNHPLLALICMAAGATVTALTCVALKK 635


Lambda     K      H
   0.320    0.137    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: 902
Number of extensions: 49
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: 635
Length of database: 646
Length adjustment: 38
Effective length of query: 597
Effective length of database: 608
Effective search space:   362976
Effective search space used:   362976
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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Protein sequences (fasta format)
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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