Alignments for a candidate for malK_Ss in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Dinoroseobacter shibae DFL-12

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 3608082 Dshi_1487 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__Dino:3608082
          Length = 693

 Score =  363 bits (931), Expect = e-104
 Identities = 223/626 (35%), Positives = 360/626 (57%), Gaps = 29/626 (4%)

Query: 1   MEEIMDS-LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIY 59
           M E  D  +L++  L+  +F +   +  V + +  V P E   + GESGCGKST+A+ + 
Sbjct: 1   MTETYDGPILEIENLSISFFTRLREIPAVMDFSCTVMPGEAMGLVGESGCGKSTVALGVM 60

Query: 60  GLLKYPGVVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMR 119
             L   G ++ G +  K +D+ +++ EELR++R KE   + Q  M +L+P  +IG Q+M 
Sbjct: 61  QDLGVNGRIVGGTIKFKGRDLNTMSPEELRRIRGKEIAMIYQEPMASLNPAMRIGKQLME 120

Query: 120 AAVSH-GVNVEEARKLIKEKLELVDLP--YNVVNMYPHELSGGMRQRVVIATSILLNPSL 176
             + H GV+ + A +   + +  V LP    ++N +PH+LSGG +QR+VIA +++ NP+L
Sbjct: 121 VPMIHEGVSEDVAYQRALDVVTDVRLPDPKRILNSFPHQLSGGQQQRIVIAMALMANPAL 180

Query: 177 IILDEPTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVE 236
           +ILDEPTT LDV V+  ++  +K + ++ G S++ ISH++ ++L   DR+ +MY+GE VE
Sbjct: 181 LILDEPTTALDVTVEAAVVDLVKDLGKKYGTSMLFISHNLGLILETCDRLCVMYSGEAVE 240

Query: 237 IGSKEEIIKRPSHPYTYLLISS--LPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCP 294
            GS E++     HPYT  L  S  LP   K    L++IPGN PL   + P  C F   C 
Sbjct: 241 TGSIEDVFDEMQHPYTQALFRSIPLPGADKNARPLVAIPGNFPLPHER-PKGCNFGPHCD 299

Query: 295 -FKMEKCSTLNPALGDIM--DGHKARCFLQKGGYVDLSTLPIPLEYYAEEKAETDLSESN 351
            F+   C   +  +  I   D H +RC         L    I      E+  +T+  E  
Sbjct: 300 YFQPGLCDAQDIRMRKIPGDDRHGSRC---------LRFEEIDWNAPVEKADQTEKPEPG 350

Query: 352 QHEVVMKILNLSKIYYIRKNLIL----SEPINAVNDVSFELKKGTITALVGGSGHGKSTI 407
           +  VV+ + NL K Y +  + +      + + A  D+SFE ++G   A+VG SG GKST 
Sbjct: 351 R--VVLNMDNLKKYYEVAASALFGGKNKKVVKANEDLSFEAREGETLAIVGESGCGKSTF 408

Query: 408 AKILAGMIQQTSGKIILLGKDVSEYGVRN-SMWYKENVQMIFQDPYSSLDPRHTVRWHVE 466
           AK+L G+   T G I+L  +++ +  +++       +VQM+FQ+P+ +L+P  TV   + 
Sbjct: 409 AKVLMGLETATDGTILLDNREIQDIEIQDRDTKTVADVQMVFQNPFDTLNPSMTVGRQII 468

Query: 467 RPLLIHKKVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEP 526
           R L I      +D    +++E+L  V  K P  +  + P +LSGG++QRV IARA A + 
Sbjct: 469 RALEIFGVGDTEDARKQRMLELLDLV--KLPRAFANRMPRQLSGGQKQRVGIARAFAGDA 526

Query: 527 KVLVADEPVSMLDASLRAGILNLIKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRI 585
           +++VADEPVS LD S++A + +L+ +  ++N  ++L+I+HD++ V Y++D +MV+Y G +
Sbjct: 527 RIVVADEPVSALDVSVQAAVTDLLMEIQRQNQTTLLFISHDLSIVRYLSDRVMVMYLGHV 586

Query: 586 VEKGNTYEVISNPSHEYTKRLIEAVP 611
           VE G T EV S P H YT+ L+ AVP
Sbjct: 587 VELGTTDEVFSPPYHPYTEALLSAVP 612



 Score =  138 bits (347), Expect = 9e-37
 Identities = 86/267 (32%), Positives = 144/267 (53%), Gaps = 18/267 (6%)

Query: 356 VMKILNLSKIYYIRKNLILSEPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMI 415
           +++I NLS  ++ R        I AV D S  +  G    LVG SG GKST+A    G++
Sbjct: 9   ILEIENLSISFFTRLR-----EIPAVMDFSCTVMPGEAMGLVGESGCGKSTVA---LGVM 60

Query: 416 QQ-------TSGKIILLGKDVSEYGVRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVER 467
           Q          G I   G+D++          + + + MI+Q+P +SL+P   +   +  
Sbjct: 61  QDLGVNGRIVGGTIKFKGRDLNTMSPEELRRIRGKEIAMIYQEPMASLNPAMRIGKQLME 120

Query: 468 PLLIHKKVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPK 527
             +IH+ VS +D    + ++V+ +V L  P++ L  +PH+LSGG++QR+ IA A    P 
Sbjct: 121 VPMIHEGVS-EDVAYQRALDVVTDVRLPDPKRILNSFPHQLSGGQQQRIVIAMALMANPA 179

Query: 528 VLVADEPVSMLDASLRAGILNLIKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIV 586
           +L+ DEP + LD ++ A +++L+K   KK G S+L+I+H++  +    D + V+Y G  V
Sbjct: 180 LLILDEPTTALDVTVEAAVVDLVKDLGKKYGTSMLFISHNLGLILETCDRLCVMYSGEAV 239

Query: 587 EKGNTYEVISNPSHEYTKRLIEAVPDP 613
           E G+  +V     H YT+ L  ++P P
Sbjct: 240 ETGSIEDVFDEMQHPYTQALFRSIPLP 266


Lambda     K      H
   0.319    0.138    0.391 

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: 970
Number of extensions: 46
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 617
Length of database: 693
Length adjustment: 38
Effective length of query: 579
Effective length of database: 655
Effective search space:   379245
Effective search space used:   379245
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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)
SQLite3 databases

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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