Alignments for a candidate for fruI in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas litoralis 2SM5

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_090276478.1 BLU11_RS13265 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo5_N2C3_1:AO356_07335
         (954 letters)



>NCBI__GCF_900105005.1:WP_090276478.1
          Length = 755

 Score =  347 bits (891), Expect = 1e-99
 Identities = 228/575 (39%), Positives = 337/575 (58%), Gaps = 27/575 (4%)

Query: 399 SGSLIQ-----AVAAAPGIAIGPAHIQV----LQAI-DYPLRGESAAIERERLQNALNQV 448
           +G +IQ     AV  APG+AIG A + +    L+A+ D  ++   A I   R   A+  V
Sbjct: 169 AGEVIQDTRFDAVPGAPGVAIGRAVVMLPPADLKAVPDKEVKDIDAEIALYR--KAVEAV 226

Query: 449 RSDIQGLIERAKAKAIRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAA 505
            +DI+ L  +  A+   E   +F  +  MLDD  L +E+   ++ G+ AQ A   VI A 
Sbjct: 227 HADIKRLSAKLAAQLRPEELALFDVYLMMLDDSSLGNEIIAGIRQGQWAQGALRDVINAH 286

Query: 506 AKEQEALQDALLAERAADLRDVGRRVLA--QLCGVETPNEPDQPYILVMDEVGPSDVARL 563
               E + D  L ERAAD++D+GRR+LA  Q  G +    P +  ILV +E+ P+ +  +
Sbjct: 287 VARFELMDDPYLQERAADIKDLGRRLLACLQEAGRQRLTFPRKT-ILVAEELTPAMLGEV 345

Query: 564 DPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDP 623
              R+ G+++  G  ++H AI+ARA+GIP ++GA     L      L++DG  G ++ +P
Sbjct: 346 PKDRLVGLVSVLGSGSSHVAILARAMGIPTVMGAVDLPYLRMDKLELIVDGNAGEVYSNP 405

Query: 624 DAATLQRAKEERDTREQRLKVAAEQ-RHEPALTRDGHAVEVFANIGESAGVASAVEQGAE 682
            +  L+R   E    E  L    E+ R EP +T DGH V ++ N G  A +A ++++GAE
Sbjct: 406 -SQELRRHYRELIREEMELSHGLEKLRAEPCVTLDGHRVPLWVNTGLFADIARSLDRGAE 464

Query: 683 GIGLLRTELIFMAHSQAPDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKE 742
           G+GL RTE+ FM   + P E  Q+A YR  L+     P+ +RTLDVGGDK L Y+PI KE
Sbjct: 465 GVGLYRTEVPFMILDRFPSEKEQQATYRAQLEAFHPLPVTMRTLDVGGDKALSYFPI-KE 523

Query: 743 ENPFLGVRGIRLTLQRPQVMEAQLRALLRSADS-RPLRIMFPMVGSVDEWRQA-----RA 796
           +NPFLG RGIR+TL  P++   Q+RA+L++++    LRIM PM+ SV+E  +A     RA
Sbjct: 524 DNPFLGWRGIRVTLDHPEIFLVQIRAMLKASEGLENLRIMLPMISSVNEVEEALHLIHRA 583

Query: 797 MTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTL 856
             E L   I V    +G+MIEVP+A   A  LA+ VDF SVGTNDLTQY LA+DR +P +
Sbjct: 584 HGEVLDEGISVPMPPVGVMIEVPAAVYQARELAQRVDFLSVGTNDLTQYLLAVDRNNPRV 643

Query: 857 SAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSI 916
           +     LHPAVLQ + +  RA    GK + VCGE+A DP A  +L+ +G D LS++A ++
Sbjct: 644 ADLYHSLHPAVLQALMLVARACREAGKPMSVCGEMAGDPAAAVLLLAMGCDVLSMNATNL 703

Query: 917 AEVKARVRELSLAQVQTLAQAALAVGSADDVRALV 951
             VK  +R++ L+  Q L   AL+  +A  V++++
Sbjct: 704 PRVKWLLRQIRLSDAQALLNEALSQDNAYLVQSIL 738


Lambda     K      H
   0.318    0.135    0.381 

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: 1302
Number of extensions: 65
Number of successful extensions: 5
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: 954
Length of database: 755
Length adjustment: 42
Effective length of query: 912
Effective length of database: 713
Effective search space:   650256
Effective search space used:   650256
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 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