Alignments for a candidate for malK_Ss in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Azospirillum brasilense Sp245

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate AZOBR_RS30440 AZOBR_RS30440 hypothetical protein

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__azobra:AZOBR_RS30440
          Length = 682

 Score =  369 bits (947), Expect = e-106
 Identities = 227/612 (37%), Positives = 346/612 (56%), Gaps = 19/612 (3%)

Query: 8   LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67
           LL+V  LT  Y +  G +   ++V+F + P E+  + GESG GKST+AMAI  LL   G 
Sbjct: 1   LLEVRNLTINYASPRGTLRAASDVSFAIRPGEVMGLVGESGSGKSTVAMAILDLLGEAGR 60

Query: 68  VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GV 126
           +  G +  +  D+  ++    R LR      V Q    +L+P   +G Q+    V H G 
Sbjct: 61  IDGGEILFEGTDLRRLSAAHRRSLRGDRIAAVFQDPFTSLNPALTVGRQIAEPLVQHKGF 120

Query: 127 NVEEARKLIKEKLELVDL--PYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184
              +A   ++E L  V +  P  +   YPH+LSGGM+QRV+IAT++  +P L+ILDEPTT
Sbjct: 121 TPRQAAPRVEELLAEVGIREPRRIAQSYPHQLSGGMQQRVLIATALGCDPKLLILDEPTT 180

Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244
            LDV V+  I++ L  +     +S + +SH++ ++  I + V ++Y  E+VE G   +++
Sbjct: 181 ALDVTVEARIIELLAGLCESHHLSALFVSHNLGIVNRICNSVCVLYGSEVVETGRTRDVL 240

Query: 245 KRPSHPYTYLLISSLPSL-VKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303
            RP HPYT  L+++LP +   RR +L SIPG     LS    SC F  RCPF  E C  L
Sbjct: 241 ARPVHPYTKGLVAALPRITTDRRHRLSSIPGTVS-KLSGASESCVFAPRCPFAEETCRRL 299

Query: 304 NPALGDIMDGHKARCFLQKGGYVDLSTLPIPLEYYAEEKAETDLSESNQHEVVMKILNLS 363
             AL     G+  RC+  +     L+  P P E  A   +    +   +   ++++  L 
Sbjct: 300 PQALRGDAAGNSVRCWKAEA----LAGTPWPEESTA---SRPQAAPPARTAPLVQVDALR 352

Query: 364 KIYYIRKNL---ILSEPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTSG 420
           K++  R+++   +  +   AV+DVSF +++G +  +VG SG GKSTI + L  +I+ T+G
Sbjct: 353 KVFGERRSILPWLRRDGTVAVDDVSFTIQRGEVLGVVGESGSGKSTIGRSLLALIEPTAG 412

Query: 421 KIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQ 480
            ++  G D  +     +   +   Q++FQ+  +SL+PR TV   +ERPL++  +    ++
Sbjct: 413 TVLFDGADFVKQAKEGNRDLRRRAQLVFQNSAASLNPRKTVGAAMERPLVLAGRQGEAER 472

Query: 481 LLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDA 540
               I  +L  VGL  P  Y  +YPHELSGGERQRV IARA A +P+ +V DE VS LD 
Sbjct: 473 -REMIAALLTRVGL--PAAYADRYPHELSGGERQRVNIARALATDPEFVVCDEAVSALDV 529

Query: 541 SLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPS 599
           S++A ILNL+   +   G+S L+ITHDIA V++IAD ++V+Y G I E+G    V+  P 
Sbjct: 530 SVQANILNLLADLRDELGLSYLFITHDIAVVSHIADRVLVVYGGTICEEGPIGRVLRPPY 589

Query: 600 HEYTKRLIEAVP 611
           H YT+ L+ AVP
Sbjct: 590 HPYTEALLSAVP 601



 Score =  152 bits (383), Expect = 6e-41
 Identities = 104/310 (33%), Positives = 158/310 (50%), Gaps = 17/310 (5%)

Query: 18  YFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLKD 77
           +  +DG  + V +V+F +   E+  + GESG GKST+  ++  L++       G V    
Sbjct: 364 WLRRDG-TVAVDDVSFTIQRGEVLGVVGESGSGKSTIGRSLLALIEPTA----GTVLFDG 418

Query: 78  KDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHGVNVE-EARKLIK 136
            D +   +E  R LR +  + V Q +  +L+P   +G  M R  V  G   E E R++I 
Sbjct: 419 ADFVKQAKEGNRDLRRRAQL-VFQNSAASLNPRKTVGAAMERPLVLAGRQGEAERREMIA 477

Query: 137 EKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILK 196
             L  V LP    + YPHELSGG RQRV IA ++  +P  ++ DE  + LDV VQ  IL 
Sbjct: 478 ALLTRVGLPAAYADRYPHELSGGERQRVNIARALATDPEFVVCDEAVSALDVSVQANILN 537

Query: 197 DLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLI 256
            L  ++ +LG+S + I+HDI+++  I+DRV ++Y G I E G    +++ P HPYT  L+
Sbjct: 538 LLADLRDELGLSYLFITHDIAVVSHIADRVLVVYGGTICEEGPIGRVLRPPYHPYTEALL 597

Query: 257 SSLPSLV-----KRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK-CSTLNPALGDI 310
           S++P L         E++L      P         C F  RCP K+   C    P +   
Sbjct: 598 SAVPRLSGAEDGPEPERILLEDSTAP----PGGGGCAFRGRCPRKLGAICDERAPPVQTA 653

Query: 311 MDGHKARCFL 320
            DGH+  C +
Sbjct: 654 TDGHRIACHI 663


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: 934
Number of extensions: 44
Number of successful extensions: 11
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: 682
Length adjustment: 38
Effective length of query: 579
Effective length of database: 644
Effective search space:   372876
Effective search space used:   372876
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