Alignments for a candidate for malK_Ss in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Phaeobacter inhibens BS107

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate GFF1398 PGA1_c14150 glutathione import ATP-binding protein GsiA

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__Phaeo:GFF1398
          Length = 695

 Score =  359 bits (922), Expect = e-103
 Identities = 224/620 (36%), Positives = 359/620 (57%), Gaps = 32/620 (5%)

Query: 8   LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67
           +L++++L+  +F +   +  V + +  V P E   + GESGCGKST+A+ +   L   G 
Sbjct: 11  ILEIDKLSISFFTRLREIPAVMDFSVSVMPGEAVGLVGESGCGKSTVALGVMQDLGKNGR 70

Query: 68  VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GV 126
           ++ G +  K +D+  ++ EELR +R  E   + Q  M +L+P  KIG Q+M   + H GV
Sbjct: 71  IVGGSIKFKGRDLAEMSAEELRDVRGNEIAMIYQEPMASLNPAMKIGKQLMEVPMIHEGV 130

Query: 127 NVEEARKLIKEKLELVDLP--YNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184
           + EEA +   E +  V LP    ++N +PH+LSGG +QR+VIA +++  P+L+ILDEPTT
Sbjct: 131 SKEEAYRRALEVVTDVRLPDPERMLNSFPHQLSGGQQQRIVIAMALMSKPALLILDEPTT 190

Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244
            LDV V+  +++ +K + ++ G S++ ISH++ ++L   DR+ +MY+GE VE GS  ++ 
Sbjct: 191 ALDVTVEAAVVELVKDLGKKYGTSMLFISHNLGLVLETCDRLCVMYSGEAVERGSIHDVF 250

Query: 245 KRPSHPYTYLLISS--LPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCP-FKMEKCS 301
               HPYT  L  S  LP   K    L++IPGN PL   + P+ C F  RC  F+  +C 
Sbjct: 251 DEMQHPYTQALFRSIPLPGADKNARPLVAIPGNFPLPHER-PSGCNFGPRCDYFEAGRCD 309

Query: 302 T----LNPALGDIMDGHKARCFLQKGGYVDLSTLPIPLEYYAEEKAETDLSESNQHEVVM 357
                + P  G+  D H  RC   +   +D +  PI +    E+K + ++      EVV+
Sbjct: 310 AQDIPMVPVQGN--DRHHTRCL--RHDEIDWAA-PITV---GEQKEKPEVG-----EVVL 356

Query: 358 KILNLSKIYYIRKNLILS----EPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAG 413
           KI NL K Y +  N +      + + A   +SFE ++    A+VG SG GKST AK+L G
Sbjct: 357 KIDNLRKYYEVSANALFDSGARKVVKANETLSFEARESETLAIVGESGCGKSTFAKVLMG 416

Query: 414 MIQQTSGKIILLGKDVSEYGVRN-SMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIH 472
           +   T G+I L GK++    + +       +VQM+FQ+P+ +L+P  TV   + R L I 
Sbjct: 417 LETATDGEIQLDGKNIEATPIEHRDTRTVSDVQMVFQNPFDTLNPSMTVGRQIVRALEIF 476

Query: 473 KKVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVAD 532
               +      +++E+L  V  K P  +  + P +LSGG++QRV IARA A   +++VAD
Sbjct: 477 GIGDSTAARRERMLELLDLV--KLPRAFADRMPRQLSGGQKQRVGIARAFAGGARIVVAD 534

Query: 533 EPVSMLDASLRAGILNLIKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNT 591
           EPVS LD S++A + +L+ +  +K   ++L+I+HD++ V Y++D +MV+Y G +VE G T
Sbjct: 535 EPVSALDVSVQAAVTDLLMEIQRKEKTTLLFISHDLSIVRYLSDRVMVMYLGHVVELGTT 594

Query: 592 YEVISNPSHEYTKRLIEAVP 611
            +V + P H YT+ L+ AVP
Sbjct: 595 DQVFAPPYHPYTEALLSAVP 614



 Score =  147 bits (370), Expect = 2e-39
 Identities = 86/245 (35%), Positives = 138/245 (56%), Gaps = 13/245 (5%)

Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ-------TSGKIILLGKDVS 430
           I AV D S  +  G    LVG SG GKST+A    G++Q          G I   G+D++
Sbjct: 28  IPAVMDFSVSVMPGEAVGLVGESGCGKSTVA---LGVMQDLGKNGRIVGGSIKFKGRDLA 84

Query: 431 EYGVRNSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVL 489
           E         + N + MI+Q+P +SL+P   +   +    +IH+ VS K++   + +EV+
Sbjct: 85  EMSAEELRDVRGNEIAMIYQEPMASLNPAMKIGKQLMEVPMIHEGVS-KEEAYRRALEVV 143

Query: 490 KNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNL 549
            +V L  PE+ L  +PH+LSGG++QR+ IA A   +P +L+ DEP + LD ++ A ++ L
Sbjct: 144 TDVRLPDPERMLNSFPHQLSGGQQQRIVIAMALMSKPALLILDEPTTALDVTVEAAVVEL 203

Query: 550 IKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIE 608
           +K   KK G S+L+I+H++  V    D + V+Y G  VE+G+ ++V     H YT+ L  
Sbjct: 204 VKDLGKKYGTSMLFISHNLGLVLETCDRLCVMYSGEAVERGSIHDVFDEMQHPYTQALFR 263

Query: 609 AVPDP 613
           ++P P
Sbjct: 264 SIPLP 268


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: 992
Number of extensions: 46
Number of successful extensions: 14
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: 695
Length adjustment: 38
Effective length of query: 579
Effective length of database: 657
Effective search space:   380403
Effective search space used:   380403
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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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